Yesterday i was having a very similar problem, i was trying to install mplayer from source and it would put the files for it in a different location then the program would look for them so i installed it with rpm's and it works fine.

Today with openbox i extracted it.

did

./configure
make
make install

no errors at all, when i do

openbox --replace

i get this error

warning: failed to load external entity "/root/.config/openbox/rc.xml"
warning: failed to load external entity "/etc/xdg/openbox/rc.xml"
warning: failed to load external entity "/root/.config/openbox/menu.xml"
warning: failed to load external entity "/etc/xdg/openbox/menu.xml"

i know the location of rc.xml is /usr/local/etc/xdg/rc.xml

any ideas why the files are being put in a different spot?

Try running it as a regular user instead of root