It happens to every craft I create eventually or on a duplicate of a launched ship.
I am on Steam although I run it via CKAN's launch KSP button. As for the save games I never get far enough to loose a great deal of progress as this happens to me very early on most game starts - on the odd occassion that I do manage to get a satellite launched it happens just shortly thereafter.
I've deleted and reinstalled the mods after replacing the original game files through Steam's file integrity checker thingy.
Mods, in no particular order:
ModuleManager, AblativeAirbrake, AlternateResourcePanel, AlternatorsForAll, AntennaHelper, AntennaSleep, TexturesUnlimited, AutoAction, AutoAsparagus, AstronomersVisualPack, B9PartSwitch, BetterCrewAssignment, BetterLoadSaveGame, CapCom, ClickThroughBlocker, CommunityResourcePack, ContractConfigurator-FieldResearch, ContractConfigurator-KerbalAcademy, ContractConfigurator-KerbinSpaceStation, ContractConfigurator-RemoteTech, ContractConfigurator-Tourism, ContractParser, ContractsWindowPlus, ControlSurfaceToggle, CorrectCoL, CraftManager, CrewLight, CrowdSourcedScience, CustomBarnKit - am curious to see if it could be this one at fault, DatedQuickSaves, DistantObject, DistantObject-default, DMagicOrbitalScience, DraggableNavball, DynamicBatteryStorage, EVAHandrailsPackContinued, EVAParachutes, FilterExtensions, FilterExtensionsDefaultConfig, Firespitter, FirespitterCore, FirespitterResourcesConfig, FlagPack, FMRSContinued, FuelEfficientPilots, FullAutoStrut, FuseBoxContinued, GravityTurnContinued, HangerExtenderExtended, InternalRCS, InterstellarFuelSwitch, InterstellarFuelSwitch-Core, Kartographer, KAS, KeepItStraight, KEI, KerbalAlarmClock, KerbalEngineerRedux, KerbalFoundriesContinued, KerbalImprovedSaveSystem, KerbalInventorySystemNoFun, KerbalJointReinforcementContinued, KerbalXMod, KIS, KSPWheel, KXAPI, Landertron, LandingAIM, MagiCore, MechJeb2, MechJebForAll, MiniAirbrakes, MissingHistory, ModActions, NavballDockAlignIndCE, NearFutureConstruction, NearFutureElectrical, NearFutureElectrical-Core, NearFutureElectrical-DecayingRTGs, NearFutureLaunchVehicles, NearFutureProps, NearFuturePropulsion, NearFuturePropulsion-LowThrustEP, NearFutureSolar, NearFutureSolar-Core, newReactionWheels, NMSG, OrbitalSurveyPlus, PartMapper, PlanetShine, PlanetShine-Config-Default, PreciseManeuver, PylonFix, RealBattery, RealChute, RealPlume, RealPlume-StockConfigs, RealTimeClock2, ReCoupler, RecoveryController, RemoteTech, RemoteTechStockConfigs, RockomaxSLSPartTextures, SafeChute, SAVE, SCANsat, Scatterer, Scatterer-config, Scatterer-sunflare, ScienceAlert, Science-Full-Transmit, ScienceRevisitedRevisited, SETI-RemoteTech, ShowAllFuelsContinued, SlingShotterReslung, SmallTweaks, SmartParts, SmartStage, SmokeScreen, Snacks, StageRecovery, StateFundingContinued, StationKeeping, StationScienceContinued, Suppliesbackpack, SurfaceExperimentPack, Toolbar, ToolbarController, ToughLove, TrackingStationEvolved, TriggerAu-Flags, TweakableEverythingCont, TweakScale, TweakscaleMakingHistoryConfigs, UICore, UniversalStorage, UniversalStorage2, UniversalStorageStockResourceFuelCell, UnmannedTech, USI-Core, USI-EXP, USI-FTT, USI-LS, USITools, VABReorienter, VaporVent, WaypointManager, WernhersOldBits, WorldStabilizer, xScience, EasyVesselSwitch, CommunityTechTree, EngineLighting, NearFutureSpacecraft, StationPartsExpansion, ConnectedLivingSpace, EnvironmentalVisualEnhancements, TexturesUnlimited-UnofficialStockConfig, ProgressParser, ContractConfigurator, ToadicusToolsContinued, CommunityCategoryKit, RCSBuildAidCont, KerbalKonstructs, Astrogator, BetterBurnTime, BetterSRBs, DecoupleWithControl, IntegratedStackDecouplers, ConfigurableContainers-Core, RN-SPP, CargoTransportationSolutions, AVP-4kTextures, TextureReplacer, CommNetManager, CommNetVisualisation, CriticalTemperatureGauge, FlightPlan, HeatControl, ScienceRelay, LCAproject, ResonantOrbitCalculator, KerbnetController, KerbalGPSRevived, ExperimentTracker, BOMPs, BonVoyage