You shouldn't be pointing Media Center at a case-sensitive filesystem.
There was a firmware bug in some NAS devices surrounding this issue. If you search here, you might find the details.
If you want to be more precise that was an upstream Samba bug
As you're finding, samba is still a finicky little beast at times, and again it's basically a case of Microsoft not following the standards correctly.
Shifting back to the issue at hand, it's a real pity and pain in the neck that Windows alone chooses to ignore case.
Whilst on a case insensitive filesystem (FAT32 or NTFS for example), case shouldn't matter, I've found cases such as the Android issue I mention above where it does, and I suspect this comes from where *Nix derived code is in use:)
IMHO it's best practice to code for case sensitivity even on a case insensitive filesystem, but obviously your milage may vary!
-Leezer-