Hmmm..... I haven't seen this problem in my own struggles, but posting the full log file may help someone else fill in the gap.
When you type in "glxinfo" you should get a line listing your rendering hardware. E.g. mine looks like:
OpenGL renderer string: GeForce4 MX Integrated GPU/AGP/SSE/3DNOW!
When AGP was acting up on my machine the line had "PCI" in the middle, rather than "AGP".
And, what do you get if you look at the contents of the files in the /proc/driver/nvidia/agp/ directory? Especially, the file 'status'. On my machine it's:
AGP Rate: 4x
Fast Writes: Disabled
It may just be my ignorance, but I'm not convinced that the XFree86.0.log lines that you printed confirm that AGP is not running. Hence, while it's unlikely I can help, I would be interested in seeing confirmation that AGP isn't running on your machine.
Life would be perfect if it wasn't for thisone small glitch....