I had this issue, there are so many random errors in the logs that they're not too informative. It turned out for me that EveBiomes was causing ContractConfigurator to go crazy during its biome scan and I was getting almost no FPS. Doing a clean install without adding it worked.
It seems when you install stuff with CKAN, removal is never clean and just messes up your game, so you pretty much have to re-install without the problem mods.
Tarsier Space Tech also had lots of Null references so I removed it, but it didn't affect the FPS issue afaik.
