I use to experience this on 2x of FF Portable, and it is still there (albeit more so) in FF3.
Anyway, I have FF set to clear private data on exit, but about 50% of the time, after the Clear Private Data dialog box appears after closing the browser; and I choose "clear private data", the window just sits there for about 30 sec., it will eventually close, but after re-opening the browser, the clear private data window will appear like I ended task on FF Portable (which I hadn't), and FF actually didn't clear anything. After then choosing clear private data FF Portable will open.
BTW, I did disable session restore upon install. I have a feeling this might be speed related, but if anyone knows of anything else (since this also happened occasionally on FF2) that might be causing this, I would appreciate the help.