Linux Mint 12: MATE confusion
MATE comes with a Nautilus port called Caja. Since Nautilus is present and updated in the GNOME 3 environment, it's not unreasonable to expect that if you so wanted, you could run Nautilus within MATE.
The issue here, though, is that Caja was launched from the Mint menu's home directory shortcut, while Nautilus was launched by clicking on the icon on the desktop. An issue like this should have been addressed prior to release.