Ship stuck in orbit, plenty of fuel, but orbit won't change

[StarkRG]

At first I thought the engine was acting like it was blocked, using fuel but providing no thrust (although mechjeb says there's thrust, just no g-forces), however even the RCS thrusters don't make any change.

The orbit is 400x160km, and when I reverted to launch and tried again I reached the exact same orbit. I know the poodle engine does work for a time because I released the lower stage so it'd fall back to kerbin and used the poodle to raise the periapsis. I was trying to get a circular 400km orbit (as I'm trying to meet up with another craft), but once the periapsis reaches 160km all acceleration seems to stop. Thrusting normal doesn't change my inclination, and radially doesn't change anything either.

I'm not sure how much this matters, but when I say it doesn't change it does a very tiny bit, thrusting prograde seems to increase apoapsis to 400.015km or so before it starts bouncing back, and retrograde reduces it to 399.980km before that also bounces back (the thrusting keeps trying to overcome the bounce, but never succeeds).

At this point I'm not sure what troubleshooting step to try next.

Mod list:

Spoiler

KSP found at /home/starkrg/Kerbal Space Program 1.1.3

KSP Version: 1.1.3.1289

Installed Modules:

- AGExt 2.0b
- AirplanePlus 3.0
- AlternateResourcePanel v2.8.1.0
- AmpYearPowerManager 1:V1.3.4.0
- AnimatedDecouplers-x86 v1.3.1
- Antennas 1.4
- AnyRes 1.3
X ASETProps 1.3
- AutoAsparagus v2.2.2
X AviationLights v3.9
- B9PartSwitch v1.4.3
- B9-PWings-Fork 1:0.40.7
- BehemothAerospaceEngineeringLargeParts 1.2.2
- BetterBurnTime 1.4.4
- Biomatic 1.2.0.0
- BiomaticForAll 1.2.0.0
- Buffalo v0.2.16
- BZ1RadialAttachmentPoint 1.0.0
- CactEyeCommunity 1.1.3.4
- CactEyeCommunityDOEPatch 1.1.3.4
- CameraFocusChanger v0.9.0.0
X Canadarm v1.7
- CapCom 2.3
- ChopShop 0.9.0.4
X CoherentContracts 1.02
- CommunityNavballDockingIndicator 1.0.1a
- CommunityResourcePack 0.5.4.0
- CommunityTechTree 1:2.4
- CommunityTerrainTexturePack 2.0
- ConnectedLivingSpace 1.2.1.5
X Contares-Antennas 1.1
- Contares-Common 1.7.3
- ContractConfigurator 1.14.0
- ContractConfigurator-AnomalySurveyor 1.6.0
- ContractConfigurator-CleverSats 1.1
- ContractConfigurator-ContractPack-SCANsat v0.6.0.1
- ContractConfigurator-FieldResearch 1.1.7
- ContractConfigurator-InterplanetaryMountaineer 1.0.2
- ContractConfigurator-KerbalAcademy 1.1.3
X ContractConfigurator-KerbinSideJobs 2.1
- ContractConfigurator-KerbinSpaceStation 1:3.2.2.1
X ContractConfigurator-KFiles 1.1.1.3
- ContractConfigurator-RemoteTech 2.0.2
- ContractConfigurator-Tourism 1.4.2
- ContractParser 4.0
- ContractsWindowPlus 6.4
- ControlLock 1.5
- CrowdSourcedFlags 1.50.5
X CrowdSourcedScience v3.0.2
- CustomAsteroids v1.3.1
- CustomAsteroids-Pops-Stock-Inner v1.3.1
- CustomBarnKit 1.1.9.0
X DatedQuickSaves 1.1.1
X DavonSupplyMod 017
X DeadSkins 1.4b
- DeepFreeze V0.22.3.0
- DestructionEffects 1:v1.0-beta
- DistantObject v1.7.2
- DistantObject-default v1.7.2
- DMagicOrbitalScience 1.3.2
X DMagicScienceAnimate v0.14
- DMTanks-AeroRTG v1.0.0
- DockingPortAlignmentIndicator 6.4
X DockingPortSoundFX v2.1.1
- EasyBoard 1.2
- EditorExtensionsRedux 3.2.14
- EngineLighting 1.4.5
X EnvironmentalVisualEnhancements 2:EVE-1.1-2-1
X EnvironmentalVisualEnhancements-HR 2:EVE-1.1-2-1
- EskandareHeavyIndustries 1.0.12
- ETT 2:v20160603
- EvaFuel 1.2.1.3
- EVAHandrailsPackContinued 0.2.1.1
X EveBiomesPlus 1.0
- FederalProductions-Flags 0.2
- FerramAerospaceResearch 3:0.15.7.2
X FieldExperience 1.0.3.1
X FilterExtensions 2.6.0
X FilterExtensionsDefaultConfig 2.6.0
X FilterExtensionsStockRework 2.6.0
* FirespitterCore v7.2.4
* FirespitterResourcesConfig v7.2.4
- FuelTanksPlus 1.10
- GAP 1.2.6
X HangarExtender 1:v3.4.8
- HangarGrid 0.3.0
- HaystackContinued 0.5.1.0
- HideEmptyTechNodes 0.4
- HotSpot 0.7.0
- HyperEdit 1.5.2.1
- Impact v1.4.2
X InfernalRobotics v2.0.4
- InterstellarFuelSwitch 2.1.0
- InterstellarFuelSwitch-Core 2.1.0
- IONRCS V0.1.3.0
- JDLiquidFuelCell 1
X JoolBiomes 1.0
X K2CommandPod 1.4
- Karbonite 1:0.7.4.0
- KarbonitePlus 0.6.4.0
- KaribouExpeditionRover 0.2.4.0
- KAS 0.5.9.0
- KeepFit 0.10.7.5
X KerbalAircraftExpansion 2:2.6.3
- KerbalAlarmClock v3.7.1.0
- KerbalConstructionTime 1.3.4
- KerbalEngineerRedux 1.1.1.0
- KerbalFlightData R21
- KerbalJointReinforcement v3.2
X KerbalOpticalAlignmentSystem 1.0.3
X KerbalStats 2.1.0
X KerboKatzUtilities 1.3.7
- Kerbulator 0.36
- KIS 1.2.12.0
- Kopernicus 2:release-1.1.3-1
- KRASH 0.5.18.1
- ksp-advanced-flybywire autodetected dll
- KSP-AVC 1.1.6.1
- KSPInterstellarExtended 1.9.4
- KSPSteamCtrlr autodetected dll
X KSPX v0.2.10.1
- KWRocketryRedux 3.0.11
- KWRocketryRedux-InstantPwr 3.0.11
- LandingHeight 1.5
- LaunchNumbering 0.2.0
- LithobrakeExplorationTechnologies 0.3.5
- LSPFlags v2.0
X MagiCore 1.1.1
- MainSailorTextures-Complete 2.0.0.0.1
- MainSailorTextures-Essentials 2.0.0.0.1
? MalemuteRover 0.1.1
- MechJeb2 2.5.8.0
- MechJebForAll 1.2.0.0
X MK12PodIVAReplacementbyASET 1.1_BETA
- Mk1RPMInternal 2.11b
- Mk2Expansion 1.7.12
- Mk3Expansion 1.1.04
- Mk3HypersonicSystems 1:1.1.0.1
X MK3InternalsApex 0.2b
X Mk3MiniExpansionPack 1:1.0
- ModularFlightIntegrator 1.1.6.0
X ModularFuelTanks 5.7.4
- ModularRocketSystem 1.12.7
- ModuleManager 2.6.25
- Multiports 1.0.2
- NavBallAdjustor 1.3
- NavHud 1.3.1
- NearFutureConstruction 0.6.4
- NearFutureElectrical 0.7.5
- NearFutureElectrical-Core 0.7.5
- NearFutureElectrical-DecayingRTGs 0.7.5
- NearFutureProps 0.5.1
- NearFuturePropulsion 0.7.3
- NearFutureSolar 0.6.2
- NearFutureSolar-Core 0.6.2
- NearFutureSpacecraft 0.5.1
- NMSG 2.0
X NoMoreGrindRedux 1.1
X notes 0.13
X ODFC 1.1
X OIFC 1.1
- OkramSA 1.0
X Olympic1ARPIcons v0.9.0
X OrbitalSurveyPlus 2.1.1
X OrbitalTug 1.2.4
X origameFoldableAssets 0.9.5.0
- OuterPlanetsMod 1:2.0
X PAPIPluginContinued v0.4.7
X PartCommander 1.1.1
X PatentPurchase 1.0
- PersistentDynamicPodNames 0.1.0
- PersistentRotation 1.5
- PersistentThrust v1.0.6
X PhoenixIndustriesBoosters 1.1
X PhoenixIndustriesFlags 1.1
- PlaneMode 1.4.2
- PlanetShine 1:0.2.5
- PlanetShine-Config-Default 1:0.2.5
- PortraitStats 9.0
- PreciseManeuver 2:2.0
X ProceduralDynamics 0.11.1
- ProceduralParts v1.2.5
- ProceduralParts-Textures-SaturnNova 1.2
- ProceduralParts-Textures-SCCKSCS 1
- ProgressParser 5.0
- QuickBrake v1.13
- QuickExit v2.00
- QuickSearch v3.02
- QuickStart v2.00
- RasterPropMonitor 1:v0.27.0
- RasterPropMonitor-Core 1:v0.27.0
- RCSBuildAid v0.8
- RCSLandAid 3.0
- RCSSounds 5.0.1
- RealChute v1.4.1.1
- RealHeat v4.3
- RealPlume 2:v10.5.1
- RealPlume-StockConfigs v0.10.7
- RemoteTech v1.7.1
- REPOSoftTech-Agencies V1.3.4.0
X RoutineMissionManager 019
- RoverWheelSounds 2.2
* SafeChute v1.9.1
- SaveUpgradePipeline autodetected dll
- SCANsat v16.3
X ScienceRevisitedRevisited 1.4.0
X SensibleScreenshot 1.2.1
- SETI-BalanceMod 0.9.6.6
- SETI-Contracts 0.9.7.0
- SETI-Greenhouse 0.9.5.1
- SETI-RemoteTech 1.0.9.0
- ShipManifest 5.1.0.0
X ShipSaveSplicer 1.1.0
? SigmaBinary-core 1:v1.5.4
? SigmaPluronKhato v1.3.0
- SmartParts 1.8.0
- SmartStage v2.9.4
- SmokeScreen 2.6.15.0
- SolarExperiment autodetected dll
- SpaceY-Expanded 1.1.9
- SpaceY-Lifters 1.13
X SpeedUnitChanger 1.4.2
X StageRecovery 1.6.4
- StationScience 2.0
- Steamworks autodetected dll
- StockalikeMiningExtension 0.93
- Strategia 1.2.4
X StrutFinder 0.2
- SurfaceExperimentPack v1.4.2
- SXT v25.2
- TacFuelBalancer 2.8
X TakeCommand 1.4.1
- TankLockRedux 0.2.1.3
- TarsierSpaceTechnologyWithGalaxies 1:6.3
- TCShipInfo 0.4
- TDIndustriesRCSandHypergolicengines 0.6
- Toolbar 1.7.12
X Trajectories v1.6.2
- TransferWindowPlanner v1.5.1.0
- TriggerAu-Flags v2.8.1.0
- TweakScale v2.2.13
- TWR1 1.30b
X UbioWeldContinued 2.3.3
- UKS 1:0.40.4.0
X UniversalStorage 1.1.0.13
- USI-Core 0.2.4.0
- USI-EXP 0.5.4.0
- USI-FTT 0.5.4.0
- USI-LS 0.4.4.0
- USI-SubPack 0.1.4.0
X USITools 0.7.2.1
- USI-UKS-Shared 0.2.4.0
X VensStylePPTextures 1.1
- VenStockRevamp v1.9.2
- WaterSounds autodetected dll
- WaypointManager 2.5.3
X WildBlueTools v1.2.8
- xScience v4.20
X YongeTechTreesPlugin 1.4

Legend: -: Up to date. X: Incompatible. ^: Upgradable. ?: Unknown 

If the craft file would help here it is.

Edited July 7, 2016 by StarkRG
Added mod list

[StarkRG]

Hmm, just looking at the raw craft file, I wonder if the issue could be caused because I created the craft in 1.1.2 before upgrading. However I did edit the craft after it had been built by construction time which should mean that it's considered to have been designed in 1.1.3...

[DDE]

I'm about to generate a report myself. It doesn't seem to be version or mod-related. It's the updated physics keeping you on-rails and thus your orbit fixed.