AE CS3 & CS4 Performance Issues related?

I upgraded to After Effects CS4 recently. Since I am in the middle of doing vfx for a feature film I kept CS3 on my computer - just in case there were any compatibility issues with 3rd party plugins and the like. I loaded a project file into CS4 to play around but it was so slow. Let me rephrase that - it was unusable. Working with 720p footage with the comp's resolution set to 1/3 quality it took over a minute to refresh the screen when I advanced the time indicator. And forget rendering - way too slow. (many layers and effects, but usually it would only take 15seconds top)

Obviously I have to stick with CS3 to finish up the film. Only now, when using CS3, it seems to be processing more slowly than usual. Not as slow as cs4 was, but still slower than normal.

Anyways, here's my question: Is this all in my mind, or is it possible that when I installed CS4 it changed some of the infrastructure that CS3 also uses - thereby causing a downgrade in performance? If that is the case, must I fully remove CS4 and reinstall CS3 - or can I simply remove certain preference and cache files? I don't have a great understanding of the inner workings of the software, if anyone can help or assure me it's paranoia, I would appreciate it greatly.