I'd like to know EXACTLY what setting you are talking about.. There's a few that might match your description.
AGP aperture - "Sidebanding" is slow, but if you have a video card with insufficient memory (32mb or less), then you may benefit from setting your AGP aperture to higher numbers.. If I understand this correctly.
AGP / PCI first boot - Neglegable difference.
AGP fastwrites - Yes
AGP 2x / 4x / 8x - Higher the better, and possibly yes.
AGP time delays - Lower latency = faster
Video BIOS shadow - On = faster
There may be other options you can change as well, but I'm sure if properly optimized, you can significantly increase your performance. At the very least, it will show up in benchmarks if you are into that sort of thing.