I just jailbroke my 3GS for the first time with 4.0.1. I installed a theme and all of my folders went away. I just cleaned it all up and d/l another theme (didn't install it) and my folders went disappeared again.
Go in to cydia/manage/packages and list out what you have installed. There has got to be something that is causing you phone to act abnormal. I had 'full preview' installed and it was causing itune to crash on open every time. I removed it in cydia and solved my problem.