Hi Brandon
I also experience of what you happened at moment you run Pkgorder on FC5. Even I try to change directory of Fedora by the other name is which I wish and also rebuild some rpm package. Moment of pkgorder which emerge only 3 file of rpm at
pkgorder.txt. I am only simple step vanished all files of temporary formed by moment of buildinstall at /tmp directory and do pkgorder return and gratify result. hopefully the way of this can assist you.
-dv
