I am having an issue with the new version RT breaking the contract system. Even with no other mods installed and with a new save game. I can accept contracts but as soon as I enter the vehicle assembly building or space plane hanger the contracts become unassigned. I have not tried is re-installing KSP 1.1.
Edit: I have tried the 32 bit version and I still have the same problem. Also I guess it is worth noting I am using windows 10.