First, thanks to willy and everybody for the replies and suggestions. I truly appreciate all the advice. (didn't want to re-quote all the posts, you know who you are) this whole group of people in this thread are just amazingly helpful folks! Thanks and sorry in advance for this novel of a post.
So upon closer examination of the jst connector, the black one (which is the troubled unit) Does seem like it's jst connector is not perfectly centered in the housing. Fwiw the black one is #4039 which I never noticed those serials either.
The white one is perfectly centered. The black one is not.
I'll need to open the black one I'm sure, I'm assuming the label comes off to expose screws on the mod Portion? (willy correct me if I'm wrong on this, I think your the only one who took theirs apart so far?)
As for the connections, the "problem" it's having, whatever it may be is not constant or absolute. Sometimes after jacking with it (swapping batteries from one mod to another and back) it does start to work, then it works sometimes for a few mi uses or for as long as a whole day but eventually it does get "corrupted" again.
Now, the black battery which I originally thought was the problem, will read extremely low voltages on the black mod during its tantrum phase, but does read correct voltages on the white mod. Now it didn't read voltages properly initially, but that battery has since been properly charged and balanced since my first day with this issue, so I can only assume that somewhere down the line I've charged the black battery on the white mod or while all the connections were good on the black one.. Bottom line I feel pretty confident at this point that the black battery is ok. I say this Because I have used the white mod several days in a row without incident and during one of the black mod attitude days even the white battery showed problems and poor voltages across the cells (and I know that battery is fine). If I Put the same battery back on the white mod and it was full and all balanced properly. Same for the black battery on the white mod, fully charged and balanced... So that can only leave the black mod section with the issue.
I'll email ecig to verify that if they needed to replace the device, could they or would they offer a refund. I have a feeling they won't have another to send. So I'm pretty sure it's up to me to fix it. I'm sure jst connectors are super common in hobby shops so it shouldn't be a big deal just a matter of doing it. I'm not worried about doing it, I'm comfortable voiding warranties.

just hate fixing an issue on a brand new device regardless of price paid.
I took a picture side by side of the jst ports, if you pay attention to the right side of the black mods jst, it's basically smooth all the way down. The white mods jst connector is centered perfectly so (as an example) if you slid a baby red screw driver down the right side you'd catch the lip of the white jst plastic as you slid it down the edge. The black one doesn't do that, you can slide all the way down without ever catching the actual white jst connector plastic piece, but the left side has a huge jst connector lip. That being off center has to explain the fact the batteries don't glide in as easily on the black dx200 as they do on the other dx200's I have. I guess maybe those pins being a tad bit off to the right make them not connect properly all the time?