I had the same problem while trying to install GTK on a debian system. I solved it copying the .pc files in /usr/local/lib/pkgconfig/ to /usr/lib/pkgconfig I never got the PKG_CONFIG_PATH variable to work. But after doing this I encoutered another problem while doing ./configure on another of the dependencies for GTK (ATK) and the error message looks like the following:
*** 'pkg-config --modversion glib-2.0' returned 2.4.0, but GLIB (2.2.3)
*** was found! If pkg-config was correct, then it is best
*** to remove the old version of GLib. You may also be able to fix the error
*** by modifying your LD_LIBRARY_PATH enviroment variable, or by editing
*** /etc/ld.so.conf. Make sure you have run ldconfig if that is
*** required on your system.
*** If pkg-config was wrong, set the environment variable PKG_CONFIG_PATH
*** to point to the correct configuration files
*** GLIB 2.0.0 or better is required. The latest version of
*** GLIB is always available from ftp://ftp.gtk.org/.
If GLIB is installed
*** but not in the same location as pkg-config add the location of the file
*** glib-2.0.pc to the environment variable PKG_CONFIG_PATH.
Now I have only installed 2.4.0 on my set, nothing else. A "find / -name glib-2.0.pc" only returns the files that has to do with 2.4.0 so how can I have 2.2.3 installed? How do I get past this?