Got any more details than "The pm popup pops up when I don't have a pm"?
Such as, does this happen after you mark all forums read, before you mark all forums read, when you come back after leaving the site without marking all forums read?
Or is it like this goddamn motherfarking vBulletin user administration script and the not-working is completely random?
Could it be that you have your browser set to OTC as the home page and someone else is using your computer while you're gone, and then they get the popup and click cancel and go on their merry way?