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/Petra backported - dualboot WIN 7
Zoom #3095 dialup USB modem