Shame it didn't help. Did you try the Safe Boot that rkaufmann87 suggested:
Restart holding the shift key until you see the grey progress bar and once booted restart as normal from the Apple menu.
You could also try a PRAM rest, but other than that I'm stuck for ideas and think it may be a trip to an Apple tech.
- Shut down the computer.
- Locate the following keys on the keyboard: Command, Option, P and R.
You will need to hold these keys down simultaneously in step 4.
- Turn on the computer.
- Press and hold the Command-Option-P-R keys. You must press this key combination before the gray screen appears.
- Hold the keys down until the computer restarts and you hear the startup sound for the second time.
- Release the keys.
The symptoms you describe could very well be attributed to RAM problems. I would suspect the possibility of an issue with the RAM modules installed in your machine. The first thing I would do is ensure that they are installed and seated properly in their slots.
Here is some info about that for the late-2009 iMac... http://support.apple.com/kb/HT3918
Also, I believe the Late-2009 iMac shipped with a set of OS and Application restore discs which included an Apple Hardware Test application. http://support.apple.com/kb/HT1883
I suggest you run the hardware tests, particularly the RAM module tests and Video or Graphics memory tests.
If you don't have the Apple Hardware Test app, use something like TechTool Pro ($).
Perhaps someone else can recommend another hardware test app.
If the RAM checks out ok after several runs, and nothing comes of the graphics hardware tests, then the issue may be software related and you'll have to troubleshoot along that line.
I hope this is helpful.