My ship is haunted! (getting control input without me doing anything)

[Jhonyrod]

So one of my ships (the only mission I'm on right now) is moving and showing like it's getting input without me pressing anything; it's not a KB/M malfunction, it's not a controller, in fact it's not any connected hardware that I can think of; it's not SAS, it's not MechJeb, I have no idea what's causing it (ok, the behaviour points to MJ, but I've reinstalled it and it didn't solve the issue). The weirdest thing of it all is that I don't have any noticeable problem while ascending through the atmosphere.

SAS or MJ's Smart ASS make it stop, but once I try to turn my ship in any direction (specially the pitch) it will try to return to a point in the navball (as far as I could see the point SAS SASS was activated on).

Needless to say I can't point my ship in any direction, I've already tried: switching to the KSC and back, reconstructing the ship, relaunching it, loading a quicksave, loading an older save, controlling the ship from somewhere else and so on.

I must mention that I have a lot of mods, in fact KSP crashes all the time from OOM issues, it does not bother me that much since the game loads quite quickly.

Here's the list of installed mods from CKAN:

{
    "spec_version": "v1.6",
    "identifier": "installed-default",
    "version": "2015.05.28.10.11.33",
    "license": "unknown",
    "name": "installed-default",
    "abstract": "A list of modules installed on the default KSP instance",
    "kind": "metapackage",
    "depends": [
        {
            "name": "ActiveTextureManagement",
            "version": "provided by ActiveTextureManagement-x86-Aggressive"
        },
        {
            "name": "DistantObject-config",
            "version": "provided by DistantObject-default"
        },
        {
            "name": "EnvironmentalVisualEnhancements-Config",
            "version": "provided by EnvironmentalVisualEnhancements-HR"
        },
        {
            "name": "AerodynamicModel",
            "version": "provided by FerramAerospaceResearch"
        },
        {
            "name": "FAR",
            "version": "provided by FerramAerospaceResearch"
        },
        {
            "name": "ModuleAnimateEmissive",
            "version": "provided by KWRocketry"
        },
        {
            "name": "PlanetShine-Config",
            "version": "provided by PlanetShine-Config-Default"
        },
        {
            "name": "Achievements",
            "version": "1.8.1"
        },
        {
            "name": "ActiveTextureManagement-x86-Aggressive",
            "version": "5-0"
        },
        {
            "name": "ActsEW",
            "version": "1.5"
        },
        {
            "name": "AdjustableLandingGear",
            "version": "v1.1.1"
        },
        {
            "name": "AlternateResourcePanel",
            "version": "2.7.1.0"
        },
        {
            "name": "AmbientLightAdjustment",
            "version": "1.4.3.1"
        },
        {
            "name": "AtmosphericSoundEnhancement",
            "version": "2.2"
        },
        {
            "name": "AutoAsparagus",
            "version": "v0.9.1"
        },
        {
            "name": "BDAnimationModules",
            "version": "v0.6.1"
        },
        {
            "name": "BetterBuoyancy",
            "version": "v1.2"
        },
        {
            "name": "ThermalMonitor",
            "version": "1.1"
        },
        {
            "name": "CollisionFX",
            "version": "3.2"
        },
        {
            "name": "CommunityResourcePack",
            "version": "0.4.2"
        },
        {
            "name": "CommunityTechTree",
            "version": "2.1"
        },
        {
            "name": "ContractsWindowPlus",
            "version": "5.1"
        },
        {
            "name": "CraftHistory",
            "version": "1.4.3"
        },
        {
            "name": "CryoEngines",
            "version": "0.1.5.repackaged0"
        },
        {
            "name": "DistantObject",
            "version": "v1.5.5"
        },
        {
            "name": "DistantObject-default",
            "version": "v1.5.5"
        },
        {
            "name": "DockingPortAlignmentIndicator",
            "version": "6.2"
        },
        {
            "name": "EditorExtensions",
            "version": "2.8"
        },
        {
            "name": "EngineLighting",
            "version": "1.3"
        },
        {
            "name": "EnvironmentalVisualEnhancements",
            "version": "7-4"
        },
        {
            "name": "EnvironmentalVisualEnhancements-HR",
            "version": "7-4"
        },
        {
            "name": "EVAManager",
            "version": "6"
        },
        {
            "name": "FerramAerospaceResearch",
            "version": "v0.15.2_Ferri"
        },
        {
            "name": "FieldExperience",
            "version": "1.0.1"
        },
        {
            "name": "FMRS",
            "version": "1.0.00"
        },
        {
            "name": "ForScienceContinued",
            "version": "1.0.3"
        },
        {
            "name": "FuelTanksPlus",
            "version": "0.10"
        },
        {
            "name": "HotRockets",
            "version": "1.0.2"
        },
        {
            "name": "InfernalRobotics",
            "version": "v0.21.2"
        },
        {
            "name": "KSPInterstellarExtended",
            "version": "1.1.13"
        },
        {
            "name": "InterstellarFuelSwitch-Core",
            "version": "1.5"
        },
        {
            "name": "IR-Model-Rework-Core",
            "version": "v01b"
        },
        {
            "name": "IR-Model-Rework-Expansion",
            "version": "v01b"
        },
        {
            "name": "KAS",
            "version": "0.5.1"
        },
        {
            "name": "KerbalAlarmClock",
            "version": "v3.3.2.1"
        },
        {
            "name": "KerbalJointReinforcement",
            "version": "v3.1.3"
        },
        {
            "name": "KerboKatzUtilities",
            "version": "1.2.8"
        },
        {
            "name": "KIS",
            "version": "1.1.4"
        },
        {
            "name": "KSP-AVC",
            "version": "1.1.5.0"
        },
        {
            "name": "ModuleManager",
            "version": "2.6.5"
        },
        {
            "name": "KSPX",
            "version": "0.2.9b"
        },
        {
            "name": "KWRocketry",
            "version": "2.7"
        },
        {
            "name": "LandingHeight",
            "version": "1.4"
        },
        {
            "name": "MechJeb2",
            "version": "2.5.1"
        },
        {
            "name": "MissionController2",
            "version": "1.12.3"
        },
        {
            "name": "ModularFlightIntegrator",
            "version": "1.0"
        },
        {
            "name": "ModularFuelTanks",
            "version": "5.5.2"
        },
        {
            "name": "ModularRocketSystem",
            "version": "1.6.5"
        },
        {
            "name": "InterstellarFuelSwitch",
            "version": "1.5"
        },
        {
            "name": "NavHud",
            "version": "1.2.1"
        },
        {
            "name": "NearFutureConstruction",
            "version": "0.5.2.repackaged0"
        },
        {
            "name": "NearFutureProps",
            "version": "0.3.1"
        },
        {
            "name": "NearFutureSolar",
            "version": "0.5.1"
        },
        {
            "name": "NearFutureSpacecraft",
            "version": "0.4.1"
        },
        {
            "name": "NovaPunch",
            "version": "2.09"
        },
        {
            "name": "PlanetShine",
            "version": "0.2.3.1"
        },
        {
            "name": "PlanetShine-Config-Default",
            "version": "0.2.3.1"
        },
        {
            "name": "PortableScienceContainer",
            "version": "1.3.0"
        },
        {
            "name": "ProceduralFairings",
            "version": "v3.14"
        },
        {
            "name": "QuantumStrutsContinued",
            "version": "1.3"
        },
        {
            "name": "RadialEngineMountsPPI",
            "version": "v0.40"
        },
        {
            "name": "RandSCapsuledyne",
            "version": "1.5.01"
        },
        {
            "name": "RasterPropMonitor-Core",
            "version": "v0.19.4"
        },
        {
            "name": "RCSSounds",
            "version": "4.3"
        },
        {
            "name": "RealChute",
            "version": "1.3.2.3"
        },
        {
            "name": "RecoverAll",
            "version": "1.2.1"
        },
        {
            "name": "Scatterer",
            "version": "0.151"
        },
        {
            "name": "ScienceAlert",
            "version": "1.8.7"
        },
        {
            "name": "Sentinel",
            "version": "0.3"
        },
        {
            "name": "ShipManifest",
            "version": "4.2.1.1"
        },
        {
            "name": "SmartStage",
            "version": "v2.6.1"
        },
        {
            "name": "UniversalStorage",
            "version": "1.1.0.4"
        },
        {
            "name": "StageRecovery",
            "version": "1.5.6"
        },
        {
            "name": "StationPartsExpansion",
            "version": "0.3.2"
        },
        {
            "name": "StockBugFixModules",
            "version": "v1.0.2d.3"
        },
        {
            "name": "StockPlugins",
            "version": "v1.03"
        },
        {
            "name": "StripSymmetry",
            "version": "v1.6"
        },
        {
            "name": "surfacelights",
            "version": "1.0"
        },
        {
            "name": "TacFuelBalancer",
            "version": "v2.5.1"
        },
        {
            "name": "Telemachus",
            "version": "1.4.28.0"
        },
        {
            "name": "Chatterer",
            "version": "0.9.5"
        },
        {
            "name": "ToadicusTools",
            "version": "11"
        },
        {
            "name": "Toolbar",
            "version": "1.7.9"
        },
        {
            "name": "TransferWindowPlanner",
            "version": "v1.3.0.1"
        },
        {
            "name": "TweakableEverything",
            "version": "1.11.4"
        },
        {
            "name": "TweakScale",
            "version": "v2.1"
        },
        {
            "name": "SmokeScreen",
            "version": "2.6.1"
        },
        {
            "name": "VNG-Parachute",
            "version": "1.2"
        },
        {
            "name": "VNG-Plugin",
            "version": "0.7.2"
        },
        {
            "name": "WaterSounds",
            "version": "1.1"
        },
        {
            "name": "WaypointManager",
            "version": "2.3.2"
        }
    ]
}

My hardware:

CPU: i7-2630QM @ 2GHz

GPU: NVidia GT 540M

RAM: 4+2 GB DDR3 @ 1333MHz

Storage: 850 EVO 1TB SATA3