jwise a04b30960c APPDEF files should be installed with mode ${NONBINMODE}, not mode ${BINMODE}.
Picked up via /etc/security:

Checking setuid files and devices:
Setuid additions:
-r-sr-xr-x 1 root wheel 252016 Nov 26 02:27:32 2003 /home/NetBSD/build/dest/i386/usr/X11R6/bin/xterm
-r-sr-xr-x 1 root wheel 4822 Nov 25 23:36:45 2003 /home/NetBSD/build/dest/i386/usr/X11R6/lib/X11/app-defaults/XTerm
-r-sr-xr-x 1 root wheel 828 Nov 25 23:36:45 2003 /home/NetBSD/build/dest/i386/usr/X11R6/lib/X11/app-defaults/XTerm-color
2003-11-26 15:18:00 +00:00
..
2003-11-22 18:01:46 +00:00