PAM misbehaving

I don't know what the hell I could have done, but on one of my boxes (Fedora Core 2), PAM stopped working. Or rather, I should say, stopped prompting me for the root password and simply not letting me use the apps unless I'm root. Most of the time it just dumps "You must be root to run this program." into the term. Some apps actually pop up a messagebox with a the same text. This is only annoying me with this one program - since pretty much everything else I call from shell and don't terribly mind SUing. I just bloody want to know how I managed to corrupt things.