I have problem that i don't see Mechjeb 2 part (AR202 pod), I'm adding part of log where is some error but i don't know anything about it :) Also on another instance of KSP Mechjeb 1 works just fine.
LOG:
Being asked to load D:/Kerbal Space Program/KSP_Data/../Plugins\MechJeb2.dll

(Filename: C:/BuildAgent/work/812c4f5049264fad/Runtime/ExportGenerated/StandalonePlayer/UnityEngineDebug.cpp Line: 43)

Non platform assembly: D:\Kerbal Space Program\Plugins\MechJeb2.dll (this message is harmless)
Loading assembly: MechJeb2, Version=2.0.7.0, Culture=neutral, PublicKeyToken=null

Part: 'D:/Kerbal Space Program/KSP_Data../Parts\MechJeb2_AR202\part.cfg'

(Filename: C:/BuildAgent/work/812c4f5049264fad/Runtime/ExportGenerated/StandalonePlayer/UnityEngineDebug.cpp Line: 43)

UnityEngine.GUISkin must be instantiated using the ScriptableObject.CreateInstance method instead of new GUISkin.