I'm running win 7 64 bit having the same problem.
From what i gather the taskbar won't autohide when there is a running program that needs attention. Some programs have settings you can change that will keep notifications from causing the taskbar to do this. Others, not so much. Unfortunately, i see no obvious indicator on the stuck taskbar telling me which program is offending.
In one case it turned out to be an outlook meeting reminder that was hidden behind several windows. Not sure why it didn't pop on top of all my windows in the first place (I missed the meeting). Perhaps I opened up a window on top of the reminder a fraction of a second after it appeared.
I have the task bar on the top edge of my screen (I work on macs too so I'm used to it being up there) It would be nice if the offending program icon blinked or had an exclamation point superimposed on it instead of covering the title bar of whatever program I happen to be working in.
Oh well. The Apple OS wasn't my idea and neither was Windows 7 ... wait, the Microsoft commercials tell me it was. Please accept my apologies everyone for making an autohide feature that doesn't always autohide. I dropped the ball on that one. If it's any consolation, Microsoft never paid me.
