Your minimized applications are likely docked on the panel. Could simply be that the "windows list" group on your mate-panel has been "compressed." Look for a small three-line icon on the panel > right click on it > move > ... then move icon around to see if your applications icons reappear.
ASUS U56E 64-bit Mint 13 MATE Maya w/Nadia backported - dualboot WIN 7
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