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Pixel Searching

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I have a question that is 1/2 related to AutoIt, but maybe some computer saavy members can shine some light on it.

In another thread, I commented on an application I'm trying to work with that doesn't return control to windows through Alt-Tab.

My scripts will be using the GetPixelColor to determine what actions to perform based on the pixels on the screen. To get around the problem of not being able to use the WindowSpy Utility, I've enlisted the help of Fraps to take full-size screenshots. These screenshots appear to have the same resolution as my current monitor settings.

So, I do the tedious task of taking the necessary screenshots of the instances and cases I'm trying to capture, then review them in Paint with the Window Spy. This gives me the PixelColor via WindowSpy and the Pixel location via Paint. I then edit my scripts to look for that pixel color in that pixel location.

If I run a script to echo back the pixel color at that pixel location when running the application "live" and I have the exact same instance currently on my screen from my test screenshots... the echoed back pixel colors do not match the ones found using WindowSpy.

After all that:

Does the GetPixelColor have a different coordinate system than the one Paint would use?

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