Yes, I have seen this as well. It appears the font increases where the background DIVS are unchanged. Definately an issue.
If possible, I would like to see an option, check box at compile time, where if checked, the EXE would ignore any off the Windows font size changes, and basically always appear at 100%. You could have the controls internally to the program that would handle the zooming, as needed. I have seen another post, that requested that the zoom functions be set and carry over between sessions. That would be a great feature as well, if it could be added.