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I'm desperate here. This has been driving me nuts for months, and it finally pushed me over the edge yesterday and I need to figure it out. When I switch from the finder to a particular app, the os sometimes does NOT switch me to that app, but another. Causes all kinds of grief – I use alt-tab to switch to an app and start typing or use a hotkey, but it's all being sent to the wrong app, and... Well, it's driving me crazy. Doesn't seem to matter if it's clicking on an app's window, using alt-tab or even another launcher like Dragthing.
Any haxies, inputmanagers, contextual menu items or other system mods installed at all? If so, disable them all and restart. See if problem is still present or not.