I’ve just managed to iron out a nasty bug in one of my FMS apps and this issue will likely affect other applications.
One of my clients noticed that some users would show up multiple times in a userlist of one of my applications. The userlist was tied to a SharedObject and users were removed from this SharedObject as they logged off. I noticed that the issue only surfaces in Internet Explorer 6 and 7, regardless of the minor Flash Player version used.
Moreover (and this was the hard bit to figure out) the issue seemed to surface only on those pages which used SWFObject 2 or SWFObject 2.1 to embed the SWF. Any pages using a previous version of SWFObject (in particular I was using version 1.5) the problem did not occur.

My conclusion is therefore that the problem somehow lies with SWFObject and how it interacts with Internet Explorer. For some reason the onDisconnect event is not invoked on FMS (I was using FMS 2 in this particular app) when my SWF was embedded with SWFObject 2.0 or above and I have now rolled back to SWFObject 1.5. Hope this helps someone as it may easily have you pulling your hair out.