I'm not an expert, but I do know that if you try to use a saved game from when you were using 3.2, that won't work. You need to start a fresh game if you change PRC version.
Occasionally, I have run across that modules that, because of their own scripting, blocked portions of the PRC from operating properly. Unfortunately, there is no fix for that problem unless someone rewrites the module.
If you are playing the OC, remember to apply PRCocfix; otherwise there will be problems.