I don't know what the AGP Memory is alluding to, but I will say that if I run a 3DMark test after a fresh boot, I will get a higher score than any subsequent test run.
According to
http://www.neeyik.info/3dmark_agp.htm, AGP memory is the same as AGP aperture. Try resetting the value in your bios, but be aware that the first test you run may be higher solely because of the system is freshly booted.
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The AGP Aperture setting in the motherboard BIOS sets the cap as to how much system memory can be devoted to the Aperture - whether your system actually uses all this memory is another matter outright. However, the setting does need to be over a certain size (typically around 12MB) otherwise the Aperture is not set up correctly and you'll lose this function. My motherboard permits 7 settings: 4MB to 256MB.
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