You've got some great responses here already Nate riddle, just had a couple of thoughts.
How much difference in battery drain are you experiencing?
If your 2 sets of batts are performing differently in the same mod, it seems to me like the issue may be the batteries. If that's not the case, I misunderstood your posts
As
@greek mule said, try cleaning your battery contacts. If that is an issue, it could solve the problem. If not, you know that isn't the issue, and it's a cheap experiment to do
I have a couple of old RX200 mods that I used a lot back in the day (and beat the heck out of). If I remember correctly the batts stayed within +-0.1 V of each other as they ran down. That still meant I sometimes had one at 3.4 V and one at 3.6 when I replaced them.
Best of luck with it Nate