what are your fuel trims? with your tuner you can data log the maf output and see if something is wrong. for a given rpm the maf signal should be very similar. if you see maf readings that dont seem right then it is the maf. it could also be a bad O2, or even a vac leak.

but yes there is a problem with being in closed loop. this points to sensors or vac leak. fuel trims should be positive if vac leak.