I've read through this thread and it looks like nobody has so far come up with a solution. The recent update a week or so ago did not fix the issue.
Here's the specs on my system:
iMac 27" i7 3.4GHz
12GB RAM, 2GB Video card
1TB Hard Drive
Third-party software:
Adobe CS5.5 Production Premium
Mozilla Firefox & Thunderbird
Asteroids 3 widget
I also have the Thunderbolt to HDMI adapter, and I'm experimenting with leaving that out to see if that's the problem (since every time I turn my TV on or off it seems to switch all the display modes on the Mac).
I'm posting a video in about an hour to show the issue.
Some apps show the menu (apple icon, various menu items, clock, etc) and others don't. Shutting down completely and restarting do fix the problem, but it inevitably (and randomly) comes back.
Hoping, like the above author, that Apple fixes this soon, because this is a huge glitch in the OS. I literally got this Mac a month ago, so it's not dying of old age.