I selected the 40k free night certificate for reaching 75 nights.

Well, it turns out that this certificate has some rule on it that you only can use it for the base room. (I'm not sure if this applies to the credit card certificates too?)
I was trying to book a property that had a base room for 34k points and slightly better rooms for 39k and 40k points. I called in and they said I can only book the base room and hope for an upgrade.

Points topup does work with this certificate, though, as long as you're booking a base room.