Okay, so you are saying battery A drains first, what happens if you swap the batteries over once the A battery is drained?
I am wondering if it's only running on 1 cell for some reason, though it does sound like a software issue as the mod needs 2 batteries to complete the circuit and will not work with a single battery in.
I do wonder about the health of your batteries, they say you shouldn't run batteries to full discharged state so that won't help the problem.
Firmware wise, I have 3 mods, my oldest is on V1.05, 2nd oldest is V1.06 and the newest RH one is V1.01 - go figure, but there must be updates out there somewhere.
Contact Smok support and try your luck and see if they reply, I got through to them on live chat once before but I can't find that option now.
If I get chance I will try and hunt down a firmware link, but I will only being trawling through Bing or Google so have a hunt for 'Smok Mag Firmware V1.06' (assuming you have the LH version).
Sorry I can't be of any more help, not had this issue and most technical support advice on here involves a hammer & dustbin when it comes to Smok