I've noticed that sometimes, if I have connected to my multimonitor PC via RDP earlier in the day and then disconnected, when I physically sit down in front of the PC later in the day, many of my applications will no longer show up on the Windows or DF taskbars.
I'm not sure how useful a report this will be as I can't consistently reproduce it (and honestly, I can't even be sure it's RDP-related, although it always seems to follow an RDP connection) but what I *think* is happening is, when I connect via RDP, Windows moves all of the windows that were on my 2nd, 3rd, and 4th monitors to my main monitor. That allows me to see those windows via RDP, since my laptop only has a single screen. I think the problem, though, is that when those windows were originally moved to my secondary monitors, DF had to hide them from the main Windows taskbar... and when Windows moved them all back to the main monitor during the RDP connection, Windows wasn't smart enough to make their taskbar buttons visible again.
Not sure if my description makes sense -- if not just ask and I'll clarify.
Obviously if the root issue could be fixed that would be ideal, but even if there was just a way in DF (maybe with a hotkey) to have it re-enumerate the window list and make sure all the windows that DF *thinks* it's managing are actually visible on a taskbar, that would work too. It just sucks having to rely on alt-tabbing to access 3/4 of your open applications after an RDP session.
BTW, I'm using DF 3.2.0 stable and Windows 7 Professional. I have a couple of dozen windows affected by this right now, so if you need a report from the Troubleshooting tab I can send one, but I'd prefer to send it privately as there is information in some of the window titles that needs to remain confidential.