Yup.
Right now, I can get my copy of HoI 2 to flicker intermittently. Why? Because I have upgraded Trillian from 0.74 beta to 3.0 basic. Having 0.74 open in the background does not cause flicker, having 3.0 open does. Version 3.0 wants to be fully visible on the desktop at all times. So, when the game starts, the current video resolution changes to 800x600 first (for the loading screen) and then on to 1024x768. Both times, Trillian wants to adjust it's window position on the desktop, calls MoveWindow to do so, and that temporarily shifts the focus from the game to the desktop and back. It goes fast enough to suppress the actual repainting of the desktop itself, but not fast enough to go unnoticed. The result is some flickering.
Like Castellon said, shut down all background tasks, especially things like messenger software (MSN, IRC, etc), and the flicker should stop. If it does not, turn your system upside down with anti spyware software, because chances are that one or more pesky spyware thingies are grabbing CPU time. That too causes flicker.
One last thing. You say flicker stops when turning down hardware video accelleration. While this can very well hide what I described above (your entire video subsystem is slower, so it also reacts slower to focus changes between programs), it can also indicate overheating of the video chip that is plagueing your system. When a video chip overheats AND has thermal protection, it shuts itself down temporarily to cool off. When it does that, the screen goes black. When the shutdown is a fraction of a second, you will perceive that as flicker.
Jan Peter