Upgraded to 3.6, now its slow!

Okay so I foolishly upgraded 3.5.7 to 3.6 by overwriting it instead of installing in a new folder.

I had previously done all the things you do to make firefox portable go fast (from following a guide online) and firefox was so fast it was better than my desktop version.

BUT now, I seem to be having an old problem I used to have where there would be intermittent pauses (sometimes lasting up to 15 seconds) in general use of firefox.

I'm sure this is a common problem, however I am unsure of how to fix it. Is there a new item in config introduced in 3.6 that makes it do it? Or is it something else? I have looked at all the FAQ's etc, and tried all sorts of things but cant seem to fix it. Can anyone help?

Edit: oh yeah, using XP and usb stick.