I just upgraded 2 blogs to 3.3.1 from 2.something
it started generating 500 error - solved it by re uploading the htaccess - somehow the htaccess code was all on one line - fixed the problem
however, the next & previous links only go to the current page (there are over 200 posts on one blog and 500 on the other.
I haven't done any code modifications and have tried a lot of things to fix this - tried alternate pagination plugins (they don't even show up)
tried switching to a twentyten and twentyeleven themes and still doesn't work.