computer resolution bug?

So one day, I turn fraps on to do some recording work for a video game (This is what I do, I record footage, I make commentaries and strategy guides and reviews)

I boot up one of these games, specifically call of duty 4 to the normal resolution which I record at it for youtube videos, 1280x720p

I notice that, once I have loaded the game, suddenly, the screen has shrunk and there are two gigantic black bars above and below my actual game screen. These two black bars are so big, in fact, that the two put together are larger than the now visible area of my computer monitor.

For games which I do not record for, I tend to play in 1280x1024, as for the monitor I use, this is optimal. I only switch to 1280x720 for my recording work. My desktop is at 1280x1024.

I wondered what was wrong with call of duty 4, as I had just the previous day recorded the game at the exact same resolution with no changes at its proper, full-screen resolution. But, this bug never went away.

I continued recording for other games. Modern warfare 2, call of duty black ops, starcraft 2, and world of warcraft for a number of months until gradually each game encountered the same bug. Modern warfare 2 came first, and now, over a year later, it has finally happened to starcraft 2.

I tried switching my desktop resolution back to 1280x720 to see if this would fix the problem, and lo and behold, my computer desktop for windows 7 64 bit ultimate has been shrunk and there are now two gigantic black bars both above and below my actual windows desktop on my monitor.

Imagine if you were watching a video on widescreen on youtube, and you switched it to fullscreen, and gained two black bars above and below the video. Now think that, but on the computer normally day-to-day with gigantic black bars hogging space and shrinking your actual computer.

The only resolution which I can properly record at is 1280x720, but the only resolution that I can actually make fullscreen is 1280x1024. This is a very bizzare bug and I do not know how to fix it.