I have this issue occasionally, and I have never found a good resolution. With some users, their apps stop creating pop-up dialog boxes. If they disconnect, and reconnect to the session, the dialog box is there and they can proceed normally. The box is not being created behind the app, I have verified that. Also when this does occur the users generally have the latest client. As a fix I have tried updating the video drivers, updating the client. Clean RE-installs of the client, and Clean re-installs of Previous versions of the client. The only fix we have ever found is to Re-install windows on the cient machine. The applications this happens in are an in-house accounting app, and ADP Timesaver. I have seen it in one or two other apps as well but not as often. I am at a complete loss for what to try next. The only consistent thing I have noted is the users seem to all have Intel based graphics cards.