When you've upgraded inserters, it can get wedged when the inserter tries to insert multiple modular armors, but the factory can only accept one (armors are unique, they never stack... but they do in the inserter, go figure :D). Haven't checked the code, and I don't know off the cuff whether you even can configure the default multiplier (factories do accept a multiple of the parts for a recipe, and I think this is hardcoded somewhere: for most recipes, it's double the parts, but for some it's 4 or 5 times... I think I've read something about this being dependent on how long the recipe takes to produce one item).

I'm super sorry about this, that's a known issue. You actually can't do anything about it, you need a special inserter/box dedicated to inserting the armour, while another inserter with the rest of the ingredients is used to insert the rest.

I actually have plans to deal with this by having new recipes for all the robots with new items introduced by the mod to add to the manufacturing side of things. I think the same issue will still happen though, if you only need 1's of something.