I've already updated to Firefox 3.5.4, yet, everytime I open it, it says it was just updated. Maybe it's because I have the 3.6 beta installed also, but I need some help here!
Both versions of FF use the same folders in the users directory. Essentially, the beta is 'overiding and reseting' the 3.5.4 settings each time you fire up the beta.
To use multiple instances / installed versions of FF, it's a good idea to have a 'portable' version that has it's own self contained folders and settings etc that won't overide your default installations settings.