This is not your issue, but just for your information in case you don't know it yet: Mapping is not saved within the composition. I mean: if you start a new composition and change mapping, the new mapping settings will be there for whatever composition you start or open. Mapping settings are saved apart.
Back to your issue, yes, Arena does save mapping settings.
Have you considered vibration? Projectors allways suffer some sort of vibration during time, no matter if it is sound, air conditioning too close, projector's fan itself, some cleaning person removing dust, whatever. This is usually what happens with me when something like this is going on. If a projector move 1mm, it might displace your projected image by 1cm, depending on distance.
Just my two cents on it.