While upgrading to 4.0-0.12 from 4.0-0.8 all the files in the /usr/lib/X11/app-defaults directory got moved to *.rpmorig and no originals were there! I had to move all *.rpmorig to * with a script. This may be due to a confusion between /etc/X11/app-defaults and /usr/lib/X11/app-defaults! FYI
This should be fixed in 0.21. Thanks for reporting.