The notifier pop-up box appears every time a user refreshes the page (or browses to another page on the site) - is this by design? I would think that once the user clicks on the "X" on the pop-up box, it should not appear again (or at least not until the next session on the site). I could easily see a situation where users want to browse the site and not read their PM right away.
From the FAQ's, it seems that the notifier pop-up box should only appear once ... judging by this sentence: set “notification type” = “DHTML Floating box” (if you choose to use java box there is no link to the inbox and every time the user changes the page they will get another aggravating popup box) the other upside to the floating box is that it is nice and small and contains a link to the inbox.
I have set the Notification Type to DHTML Floating Box. Anything else I could check on. (Sorry if I've missed something ... have searched the FAQ's and this forum as well.)