OS filename issues and checking in code reminds me of an 8-hour mess I got myself into due to OS X deciding that filenames are case-insensitive, and git knowing that they are not...
I have had funny experiences copying files from Linux to a NTFS partition, because NTFS is actually case-sensitive, but Windows itself is not, so you suddenly end up with two files that differ only by case and you can't delete or rename them (but funnily enough they show fine on Explorer).