My guild is also having a big problem where the MT window cannot be dragged even when holding down alt. They've tried clicking all over and it doesn't work. I had it happen to me but when I switched to windowed mode (on my Mac) I was able to move the bar. They've tried reloading ui, logging out and back in, and also made sure to be at the newest version.
I got this solution from the EJ forum.
Do your guildmates use ag_unitframes? If they do, make sure they don't have hidden raid frames, because thats what it was for me. The aguf raid frames will default be hidden over where you have to click to drag the MT and PT target boxes. Un-hide the aguf raid frames, and move them somewhere else. Then you can freely move the MT/PT boxes.