So, I'm having the same problem. But, I don't think it was the different armors causing the problem. Would the Mod Armor Pockets mess with it possibly? I only mention it because that was one of the few mods I added right before it happened to me as well. Once when I died and went back to pickup my armor off my body and the inventory slots no longer where there and another time when I tried to upgrade to another type of armor (Nuclear Fission Armor).
Great Mod! Look forward to your thoughts regarding the above. Thanks