If your mod is running in series, not parallel, (which I think many if not most do but I am hazy on this concept?) I guess this could make sense... The battery is still being used, even if the mod is not showing it as fully charged when you fire...? With that said, I'd still hope to remedy the problem, so I hope your vendor gets back to you regarding the issue. It seems so odd that a mod would read a battery as dead but still fire it, but honestly when it comes to electronics I am a total twit, so I wouldn't be the best person to ask. I'm wondering if it could be an arcane *setting* thing you are running into, but again, I'm not familiar with the mod, so I couldn't really say.
Best of luck with it! To me, it sounds like the electronics are going a bit haywire somewhere. I'd be hesitant to run the mod, but I tend to be ultra cautious with that stuff. May want to look at some YouTube demos online, though, to rule out a settings issue (though I cannot see any rationale for having such a setting, but perhaps there is one... IDK).
Anna