The user's file permissions were set wrong on /usr/lib/pt_chmod. The user had:
# ls -la /usr/lib/pt_chmod
---s--x--x 1 bin bin 3120 May 3 1996
The permissions should be:
# ls -la /usr/lib/pt_chmod
---s--x--x 1 root bin 3120 May 3 1996
Note that the owner should be root, user had bin as the owner. Also note that the setuid bit must be set. Once the user did a chown root pt_chmod, everything worked again.