OK, this is weird. At first this trick didn't work.
I deleted the old file, run FF, logged in to a few sites, CC detects them not.
However, when I closed FF 3.5 and run CC afterwards the cookies were picked up!
To save any cookies I need, i have to wait until after I closed down FF3.5.
Installed final Firefox 3.5 and the problem appears to have gone away.
I think the cause was the fact that beta versions of Firefox 3.5 were installed in Mozilla Firefox beta x instead of just Mozilla Firefox directory.