I've noticed that when I get the pop-up, and I go view the message, and then go back to the main forum listings by using the "back" button, the pop-up re-appears. That's because the cached version of the webpage for the main forum listings includes the PM notification pop-up. I have found that I can avoid this by not using the cached version, and instead either (a) going to the main forum listings directly, or (b) if I get there using the "back" button, I refresh that page and the refreshed version no longer has the pop-up.