I may be wrong in this one but I think nVidia's Makefile is broken and it doesn't check whether or not nv-freebsd.h has been modified. If you just modified it and 'make setup' you may had installed the module wich uses nVidia's AGP. Try to 'make clean', modify nv-freebsd.h and then 'make setup'. Failure to detect your hardware is may be caused by this.
Hope it helps.