Docked capsules keep disappearing!

[Maelin]

I've been having trouble with docked craft vanishing when they reload. It happened with my Mun lander and I had to go through a bunch of annoying fiddling and save editing to get everything back, and now it's happened again. Basically I launched a station with a 3-person capsule on the front, then I detached the capsule, swung it around and docked it to a docking port on the side of the station. When I launched a small probe to take a science experiment up there, I came close and realised the capsule had vanished. Here's a screenshot I took of the thing successfully docked before I unloaded it to go build and launch the experiment module: imgur link

Here's the output_log.txt file. I don't expect a solution straight away, but rather I'm hoping someone can give me some help interpreting the output_log, so I can get started working out what is causing the problem and how to fix it. The things I noticed that seemed relevant are at line 81213 where there's a bunch of orbital values that are all NaN, and shortly after that on line 81489 where it says:

[ProtoCrewMember Warning]: Crewmember Jebediah Kerman found assigned but no vessels reference him. Jebediah Kerman set as missing.

But I don't know what to look for in the stuff beforehand to work out why it isn't loading the docked module. Any suggestions? (On a side note, what's the simplest way to get KSP to make regular backups of its save files? Any mods that do this?)

Here's my modlist (tidied up export from CKAN):

• AGExt, ver: 1.32d
  
• ActiveTextureManagement-x86-Basic, ver: 5-0
  
• BDAnimationModules, ver: v0.6.1
  
• CapCom, ver: 1.1
  
• Chatterer, ver: 0.9.5
  
• CommunityResourcePack, ver: 0.4.2
  
• CommunityTechTree, ver: 2.1
  
• ContractConfigurator, ver: 1.3.4
  
• ContractConfigurator-ContractPack-SCANsat, ver: v0.5.2
  
• ContractConfigurator-FieldResearch, ver: 1.0.4
  
• ContractConfigurator-RemoteTech, ver: 1.1.4
  
• ContractsWindowPlus, ver: 5.2
  
• CrowdSourcedScience, ver: v3.0
  
• DMagicOrbitalScience, ver: 1.0.4
  
• DeadlyReentry, ver: v7.1.0
  
• DistantObject, ver: v1.5.5
  
• DistantObject-default, ver: v1.5.5
  
• DockingPortAlignmentIndicator, ver: 6.2
  
• EVAManager, ver: 6
  
• EditorExtensions, ver: 2.8
  
• HyperEdit, ver: 1.4.1
  
• IR-Model-Rework-Core, ver: v01b
  
• IR-Model-Rework-Expansion, ver: v01b
  
• InfernalRobotics, ver: v0.21.2
  
• KAS, ver: 0.5.2
  
• KIS, ver: 1.1.5
  
• KSP-AVC, ver: 1.1.5.0
  
• KWRocketry, ver: 2.7
  
• KerbalAlarmClock, ver: v3.3.2.1
  
• KerbalConstructionTime, ver: 1.1.7
  
• KerbalEngineerRedux, ver: 1.0.16.6
  
• KerbalJointReinforcement, ver: v3.1.3
  
• ModularFlightIntegrator, ver: 1.0.repackaged0
  
• ModuleAnimateEmissive, ver: v1.3
  
• ModuleManager, ver: 2.6.5
  
• PreciseNode, ver: 1.1.3
  
• ProceduralFairings, ver: v3.14
  
• RandSCapsuledyne, ver: 1:1.5.1
  
• RealChute, ver: 1.3.2.3
  
• RemoteTech, ver: 1.6.5
  
• SCANsat, ver: v12.1
  
• ScienceAlert, ver: 1.8.7
  
• ScienceRevisitedRevisited, ver: 1.3.0
  
• StageRecovery, ver: 1.5.6
  
• StationScience, ver: 1.5
  
• StockClamshellFairings, ver: 1.0
  
• TACLS, ver: v0.11.1.20
  
• TACLS-Config-Stock, ver: v0.11.1.20
  
• Thermometer, ver: 1.0.8
  
• ToadicusTools, ver: 13
  
• Toolbar, ver: 1.7.9
  
• TurboNisuReloaded, ver: 2015-05-06
  
• TweakScale, ver: v2.1
  
• TweakableEverything, ver: 1.11.6
  
• UniversalStorage, ver: 1.1.0.4
  
• kOS, ver: 0.17.2

- - - Updated - - -

Followup: I just discovered that my last quicksave was on the station, after docking. When I quickload, the station loads up, and the capsule is still there docked on the side for a fraction of a second while it's loading, but then the capsule vanishes immediately as the it finishes loading and everything starts moving. So my quicksave still has the capsule docked there, but something is going wrong when it tries to load it.