Yeah, seems it doesn't occur on every system.
Just reverted the .ini change to test this, and when I restart it in windowed mode, I... can't see it because it got covered by stuff. :s
I think I'm seeing some patterns now, I know when it will happen.
Eg., if the windowed FormSize is such that the size of the Artist Pictures element will be equal to whatever size it is when the form is fullscreen, then no glitch will happen, even if I restart it in full mode (just tried).
If I resize the window (make it smaller) so that it resizes the Artist Pictures element, part of it gets obscured by the element below it (Track Information's cover).
It's the obscured part that ends up showing glitched.
Few pics to illustrate:
1. Fullscreen, all working fine. Artist pictures on the upper-right. http://imgur.com/GDCFhIg
2. Going windowed and resizing. Notice how the artist photo got obscured and only their heads are visible. http://imgur.com/2KNUoY1
3. I switch to fullscreen, and restart MB. When it opens, the obscured region of the image is now transparent and displaying a still of the window that was underneath (web browser), the unobscured portion of the image is displayed fine. http://imgur.com/2Qzp8xZ
Guess I got my solution now, your reply clarified it a bit for me. Too much information on my screen to ever use windowed mode so I never noticed this, now I know to keep it at the right size.