Wow! That's amazing. I had something along those lines happen to me once (different app and black boxes in different places but still). Anyways, maybe:
1). Go to the .exe's properties and under compatibility, check "Disable Visual Themes" & maybe play around with other compatibility settings if that doesn't work.
2). Update DirectX 9 (or any others Tree Magik uses) and any display drivers you are using.
3). Are you using any abnormal display settings? I noticed it's only where Windows-rendered fonts appear. Maybe this is a clue in trying to resolve the problem.
Hopefully this'll at least help with the process of elimination if it doesn't help resolve the problem.