Thanks for the video and feedback. That is really odd.
The close button is the right size, the restore button is squashed, and the minimize button does not exist. In addition, the hover background is an equal size for all of the buttons but sized for the Windows 7 Aero theme. This is even odder because the hover background is directly based on the button image size. Considering that the button sizes/images are determined on startup using a single Windows API call that should return reliable sizes, and not recalculated later unless there is a system setting change, and the fact that you noticed it change later on after startup, makes this even stranger.
Is it possible that a DLL you are using is interfering in some way?
Is it possible that you changed a system setting, such as colors, themes, DPI, etc.?
I am going to add some debugging to the next beta to try to see if this can be tracked down.