an example is here with navit it doesn't find libgps.pc which is present in the system exporting the pkgconfig variable into .bashrc made the program compile
Try to come up with a simple way to reproduce (other than trying a software which isn't in Portage)
Otherwise I'm inclined to believe this is a problem in the package, not pkg-config
As far as I can tell, libgps.pc is installed by sci-geosciences/gpsd.
app-portage/pfl's e-file lists /lib64/pkgconfig/libgps.pc as one place where the .pc file might have ended up erroneously (in past times, I expect). Maybe this information helps you.
*** This bug has been marked as a duplicate of bug 176552 ***
Ah, there we go.
*** This bug has been marked as a duplicate of bug 401021 ***