Ok, I got something. The capsule flower in additional turrets automatically removes ammo as it is inserted if it is not of a certain type. This causes the ammo loader to endlessly attempt to load ammo that continuously gets rejected. I'll have to do some serious tinkering to get this working fully.
Additionally, some turrets use normal chests as ammo holders, and I will have to make several extensions to get these supported. In short, getting these added could take a few days.
The good news is that I've implemented a temporary solution in config.lua in the form of an ignore list. The ammo loader still won't work for Howitzers, Capsule Flowers, or Destroyers, but their presence should no longer hinder it in loading all other turret types. Apply update for the changes.
Also, thanks for the info about supremewarfare and friends. I'll go check those out as well.