I had a similar problem with my laptop and the answer in that particular case was the screen itself.
When the screen light starts to fail it will cause the screen to flicker. it might eventually even get worse and black out intermittently. The only solution is replacing the screen in this case.
Second possibility is the video card. but that's a long shot. Some warranty repair shops have the appropriate software testing benchmarks that they can run that will "stress test" all the internal components of your laptop. Thus, they will be able to evalute the results and take the necessary steps to replace the faulty hardware.
In my vast experience in tech support, I haven't seen software causing screems to flicker.
Another possibility could be EMI. or Electromagnetic Interference. Something as simple as a microwave, proximity to a lightbulb, or even a cell phone nearby could cause the screen to be affected as you described.I will definately take advantage of that warranty you still have.
Keep me posted.
Cesar
MCSE, MCP, A+, Webdesigner