It's unlikely considering the timing, but check the batteries to make sure you don't have a dropped cell in one of them. I had a similar issue and when I unhooked and isolated both batteries and let them sit overnight one was resting at <10v.
Otherwise check for belt slip and loose or improper wiring at the alternator. Check the voltage at the alternator if possible and along any points in the wiring to the batteries to make sure the connections aren't loose. If everything checks out contact the alt manufacturer and see what they have to say about it. I would NOT try a boost module as a bandaid to cover up a potentially bad alternator.