Can you please upload your system configuration? Help->System Info operator would help you collecting it. It can be video driver issue, especially if it's intel videocard.
What you may want to test is to change Window Draw Method in User Preferences->System page. Also, maybe it's possible t upgrade your video driver (say download latest driver from nvidia.com if you're using nvidia card).

I attached system info text file.

As for vid drivers, I recently had the latest nvidia drivers installed when I was playing around with cycles, and I recall it being the same issue. As for my prefs, you are right, it seems to be "overlap" mode that causes it. Setting it to auto it goes away, and overlap brings it right back.

Please don't nerf overlap, it makes the 3d editor feel snappier! :)

We've got Auto draw method by default and don't think nerf of overlap is good idea -- for other cards/drivers it can be the only working solution.
If i understand you correct, changing window draw method helped for you, so will close report. If i misread you, please write back here and i'll reopen it.

DIscussed this in IRC. Changing draw method isn't a full fix. Re-opening and moving to OpenGL tracker.

Moved from Blender 2.5 Bug Tracker to OpenGL errors

I was taking a look at a debian bug report on this at:

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=639446

I looked to see if it can be reported as closed there or not, and did some tests.

The latest trunk, and going back at least as far as the same revision reported, r41759, all seem to have no flickering for me in linux any more (overlap or auto mode). I have upgraded to ubuntu 12.04 since reporting though, so I have no idea what specifically could have fixed this issues (libs or GPU drivers etc).

Either way, 12.04 the problem seems gone for me now, so I am no longer able to (easily) verify when this is actually fixed since it disappears. I will also see about pointing the debian bug here as well so they can at least track the status of the problem as well.

o/