Some websites use FF2.0.0.20 profile, for 3.0.5

My situation is pretty unusual. The Flash drive is doing ok, but I like so much FF portable that I have FF3.0.5 installed on my hard drive, and made it default. FF3.1 beta2 coexists, beautifully, with 3.0.5, but there are problems, with two websites, so far, who open/use 3.0.5, but with the profile of 2.0.0.20, which is not portable. Aside for the unusual mix, should I go portable all the way, and do away with the conventional 2.0.0.20.
I understand that it is an unusual situation, but I like the idea of keeping more than one version, because of the different bookmarks and add-ons.