I still have this issue. I keep setting the non SEF filters in the backend, but they work for a test run, and after a day or two userrs start complaining again - simply they stop working, and joomSEF keeps redirecting them to users/activate
Joomla! 2.5.6, version 4.2.7
I use JoomSEF, because it works with more extensions, but with that issue it makes the site useless. Buying support also seems a bad option, as I see a lot of people complaining, that it isn't worth it :(
Also, when I enable JoomSEF - the registration confirmations sites don't appear, their simply blank sites.