I have the same problem and have had i for some time. I tried to find a pattern to it but it seems to be the same as you said. It happens after I close a panel of some sort.

I had a new symptom today when I tried to reproduce the problem and changed my screen setting (I have an nVidia GTX 275 an uses two screens at once with deskop stretch horizontally across both) to only use one screen and this time the problem happened immediately after I fought a spider (two turns into the game) and closed the battle result dialog. This time, however, even the little bar at the bottom disappeared on me. I managed to get that back by exiting to the main menu and then returning to the game. The "proper" GUI was still missing however.