I haven't had this problem, but I also haven't used WDC for map editing much (I use ChaosEdit normally).
Looking at the WDC thread, I think its the bug where when you click dialogue boxes, sometimes it will make modifications to the map behind it. Not certain, but this seems kind of like what is happening. ChaosEdit won't work for me because there is no zoom feature.
I am giving Havoc's Editor a try. I like the interface pretty well. Can't figure out how to get statistics for individual items though and that is kind of a must-have feature. I am sure it is there and I'm just overlooking it.