Is it just one update announcement?
I had exactly the same problem and resolved it once and for all by discovering the unannounced update and letting it run. I suspect it is just that one Microsoft update that causes this. Once it updated, the problem was gone. Find that guy and fire him! Or maybe he was on the way out and this was a parting 'gift'.
Why it's stuck determines the fix
I well remember this problem in XP, where I had to use the off/on trick with the Autohide setting to get it working right.
In Windows 7, I've not encountered the "invisible message bubble", but I have noticed that sometimes a window will open up that wants direct attention, and until it gets it, the taskbar stays open. For me specifically, this would happen any time I download from the Internet via Firefox (up through v10; haven't noticed it in v11). Once the Download Manager window opened, the taskbar wouldn't close until I clicked on the DM window.
You can tell if you have an open window issue by looking on the taskbar--if one of the open program tabs is orange, that's an active window that wants your attention.
Windows 7 Taskbar won't autohide
Thanks lounger. Seems Microsoft didn't remember they built in a way to flag us about updates. You were absolutely right. All you have to do is check your notification area and there is probably just some Windows Update ready to install. As soon as I allowed it to start, my taskbar went away. Good job. Was a point of frustration for me as well and it is resolved.
Notification Area Icons settings
I, running Windows 7 64-bit on 3 machines, have not had that problem, though I did with 2000 and XP. Perhaps the reason is that I went into Control Panel → Notification Area Icons and made sure that every icon was set to either "Show icon and notifications" or "Only show notifications". From what others have said, it seems that the other option, "Hide icon and notifications", would be conducive to the problem. I don't know whether this is relevant (sorry if not) but it's worth a try.