I'm not sure that Media Center is completely to blame here. I often find that if I rename a file/folder in Explorer just to change the case, when I refresh the view it's back to what it was before.
Windows should be case-preserving.
+1 if this could be looked at and corrected. It has tripped me up more than once when doing a quick RM&C w/o doing a Clean first. If I manually edit in Windows Explorer, it fixes it, but then obviously re-Imports the Files. Granted, I'm usually in Windows Explorer any way since I have to manually move Cover Art, rip logs, recording logs, etc (hint, hint).
The issue seems to only effect Filename (path), not Filename (name).