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Similar thing happens to me about once week as well - altdesk mysteriously hides behind the taskbar. I didn't report it because I can't reliably reproduce it. Whenever it happens I open a media player like KM-Player or Media Player Classic, press enter (which toggles the fullscreen mode of the player) several times and click to a different application window. Then my altdesk appears on the top again. Anyway as it doesn't happen very often it doesn't bother me much.

By the way the tool I have used before you implemented this feature (http://www.sevenforums.com/tutorials/54842-taskbar-always-top-disable-enable.html) has the same bug as well. Well more like had, after some windows updates the tool doesn't work at all.
RaMMicHaeL I'm afraid it doesn't work for me. I have an application with activated "always on top" setting and I've set the taskbar tweaker disable_topmost feature to 1 (and rebooted my PC to be certain). Then I can drag the application above the taskbar. However when I click on the taskbar, the application immediately hides behind it which should not happen. I need the application to always stay above the taskbar.