In LR 2.5 I have always loved the fact that filters ( ratings, flags, etc ) stay they way you leave them (sticky) in each folder. This WAS great because each folder in my catalog are in various states of selection. WHY oh WHY has this ability been taken away in LR3B2??? Why is this being touted as a new feature?
Let me explain then that many people hated the way filters were sticky. Within a session, I agree it often made sense that you could switch between folders and their filtration remained. However, it's not the same when you revisited those folders days or even months later - your first reaction would be one of "where the f£c9 are my pictures" panic. Plenty of people complain that their pictures are gone, gone, gone - while less panicky folk would have a few seconds of disruption. I would have preferred LR3 to have a "purge all filters" command or an expiry preference (non sticky, sticky forever, session-only, x days), but I regard the non-stickiness and the lock as a huge improvement.
Another point is that filters are designed to be an inherently temporary filtering of the images shown - ie not an organisational tool. If you routinely leave folders filtered, then it's usually an indication that you are using folders too much and aren't making as much use as you should of smart and dumb collections .
John
Have you tried going back to a previously-filtered folder and pressing Cmd L / Ctrl L. It may do something.