I've had something remarkably similar to that happen with pidgin in the past, though the problem showed up in a different manner - fullscreen didn't work correctly in my case.
Quite simply you have an application that is docked but somehow is invisible, but your system knows its there and acts accordingly. As such, your mouse is acting on the invisible application rather than the visible one. A quick fix would be to kill the application from task manager and restart it. Pidgin eventually fixed that bug, so chances are once the devs work out its a problem, it will be taken care of.