OK, got further info for you:
The following in the spoiler is outdated information:
Ok, now I pinpointed the issue and I know why nobody reported it.
The bug appears, if you equip 2 iron swords, then equip a iron war axe and then unsheath your weapons. If you haven't had the 2 iron swords equipped before, everything works perfectly fine.
If you want to, go ahead and fix it, but honestly, this is a really minor issue. From me this mod gets a go.
I could reproduce this glitch with every one-handed weapon (only iron weapons).
1. Enter combat mode(unsheathe your weapons)
2. Equip 2 times the same one-handed weapon X
3. Equip any other one-handed weapon Y in your RIGHT HAND.
4. You now have X and Y in your hands, while another X is sheathed.
Also this glitch only works when Y gets equipped in your right. If it gets equipped in your left everything works fine.
Thanks for the info. I'll look into it when I get home and release a patch if it happens to me as well.