Currently once you click one of the items in your notifications and the page loads it is removed from your list of notifications.
In the case of JomSocial this is not a positive feature. Obviously I have a link to point to the author, so the individual with the notification has easy access to the authors profile. However, if the receiver clicks the authors name, and then wants to open the notifications again to click the link to the action they can't, because that item is no longer available. This is mainly a pain when Friend Requests have been notified. In many instances the receiver would want to first click on the Author's Name and see their profile, and then open up the notification box again, and click on the action link to accept it.
Simple reproduction of "issue":
1. User X Sends User Y a Friend Request.
2. User Y Opens notification box, clicks on User X's name to view Profile.
3. User Y Opens notification box to click on the action link (Friend Request) but the entire notification is gone.
Not sure what the best solution is, but maybe the Administrator could specify X number of minutes for item to stay in notification area.
***Important side note.... When I say for the notification to remain in the Box I mean exactly that. The Red Notification image with notification count should disappear once clicked. Only the markup inside of that box should remain for X time. Any notifications after clicking on Red Notification image should begin new count.