I have been having same issues as well.
Made the mistake of booking a 2 night reservation with one on points (40K) and one with the 75N certificate.
First agent attached the certificate but it still showed taking 80K points (although as a points advance, so it did not actually deduct anything).
I called in 3 times to fix, every time the agent claimed it was fixed. Finally called in a 4th time and the reservation looks different, but the agent said wait 48 hours for it to show correctly.
I feel sorry for the agents since they did nothing wrong, and it looks like a systematic issue.