[Peter Ebbesen]

Militarist, there are some known bugs in Dom3 still. One of those is losing certain weapon slots when you equip a commander with several inherent weapons with new items.

I don't know the mod you are talking about so I don't know if your specific case matches the general case, where a commander with a mix of melee or ranged [or just plain weird] weapons loses his inherent non-melee weapons when an 1H weapon is equipped in the first hand slot and regains it when a shield is added to the second hand slot - but does not regain it if done the other way around) but it might be worth trying out.

If you have not done so already, I would advise you to read the bug shortlist one of these days. There are some really weird stuff in there, which hasn't been fixed yet (and possibly never will).