This bug has been reported here: https://bugzilla.ubuntu.com/3060

"On a fat32 partition if I create a new folder (via a right-click) using
Nautilus, and gives it a name using only upper-case characters, lets say "TEST",
2 folders will be created: "TEST" and "test".  But after a reload, using ctrl-r,
Nautilus will then only display one folder named "test"

If I look on the fat32 partition using an xterm session, only one folder is
present "test", even when Nautlius is displaying both "TEST" and "test" (before
the reload)."