Q: Flashing Menu Bar

Don't you by any chance have one of those Facebook notifications menubar applications?

If so, try disabling them.

I have the same problem. Everything is updated and those apps who don't run in Mountain Lion i have removed from my Imac. Can't find what causes the problem but its annoying.

So there more people out there with the same problem so there must be a sollution.

Did you find a solution to this problem? Is this what's happening?

https://www.dropbox.com/s/cnl8j49456k56uc/menubar.m4v

Please let me know. LIke you, I'd hate to do a clean install for a problem that is only a nuisance.

If the problem is still there, try booting into the Safe Mode.  Disconnect all peripherals except those needed for the test. Shut down the computer and then power it back up. Immediately after hearing the startup chime, hold down the shift key and continue to hold it until the gray Apple icon and a progress bar appear. The boot up is significantly slower than normal. This will reset some caches, forces a directory check, and disables all startup and login items, among other things. When you reboot normally, the initial reboot may be slower than normal. If the system operates normally, there may be 3rd party applications which are causing a problem. Try deleting/disabling the third party applications after a restart by using the application uninstaller. For each disable/delete, you will need to restart if you don't do them all at once.

Safe Mode

Safe Mode - About

General information.

Isolating issues in Mac OS X

Troubleshooting Permission Issues

Step by Step to Fix Your Mac

I did happen in safe mode. What I did was disable the spotlight icon. Spotlight is still enable, but for some reason the issue was the spotlight icon itseld.

http://hints.macworld.com/article.php?story=20091030173117381

Hasn't happened since.