I was having major problems with this when reverting to VAB and occasionally when deselecting parts in VAB construction. I have resolved this issue. I realised that this is the same issue I was having pre 1.1 because VAB can cause a jump in memory usage taking the game over the x32 memory cap.
I took a look at my task manager and found that the process was KSP.exe *32 so for some reason my game was still running the x32 application rather than the x64. To resolve this I went to the game files and renamed KSP_64.exe to KSP.exe.
This appears to be an issue stemming from my steam not giving me the option to launch in x64.
Hope this helps others.