Just add this to your popup menu to unload and reload the hotspots:

*Popup "Hotspots" Folder
*Popup "Hotspots On" !ReloadModule $ModulesDir$ckHotspots.dll
*Popup "Hotspots Off" !UnloadModule $ModulesDir$ckHotspots.dll
*Popup ~Folder

Change ckHotsots.dll to hotspots.dll if thats what module your using.
I've been doing this with games for awhile now, though some games don't cause a problem, also if the resolution for the game is smaller then your desktop area this won't happen.
Hope this helps.