From the descriptions you have provided, it seems to be either the windows Aero peek setting or possible hardware issue. Please provide the model of the computer you are referring to. Also does it happen in all windows(safemode) and applications? If you did not get a chance to try in safemode, please do so. Also try to scan your computer for related software failures and or spyware/viruses.
Seems this problem continues to happen. Its been happening on my Sony Vaio Touchscreen, much to my annoyance. I installed a program that logged what background program was constantly minimizing my screen. (every 5 to 10 minutes) It turned out that it was coming from the sensor on the bottom left of my touchscreen. Generally you touch that point on the screen if you want to minimize programs and return to the desktop. It was periodically being triggered WITHOUT me touching it. I first turned off the mechanism that enables the touch sensitivity (In the Control Panel) and the problem disappeared, so it was definitely coming from something related to the touch sensitivity. I turned the screen sensitivity back on and the problem returned.
I then took a screenwipe and cleaned the area over the sensor and it stopped misbehaving. Some dirt was evidently periodically triggering it. Its now behaving just fine.