I found the beta version of Firefox 2.0 initially grabbed hold of the existing 1.5 Profile and disabled a few extensions. It was OK after a separate Profile was created for Firefox 2.0. After that, one Profile or the other could be selected in the Profile Manager when starting up each version of the browser.
Alternatively, a couple of .bat files can be used to make the browsers start up independantly of each other without the need to use the Profile Manager. Firefox 1.5 and Firefox2 Beta 2 can even both run at the same time (if you want them to), each one using its own Profile. I found that best in the end.
Instructions here on how to set it up.