I had this many times before and never had any of my models a problem.... I don't now how to fix this, maybe it's more or less "natural" but it seems that the badbcounts have no negative effect in-game.
EDIT:
I checked Bethencourts and wangrins 3d modeling tutorial, they did not mention it so I doubt is it a problem especially as you have no possibility to find the issue
EDIT 2:
I even get badTcounts when I simply use the converter you used to convert a vanilla model to ms3d and then backconverting it to .variant_weighted_mesh