The bot settings thinks that ammo bags count as empty space and won't return to town or stop farming, etc because it thinks it has open bag slots. Plz advise. 

In the settings there's an option to set on how much free bag space it should go to vendor.

If your ammo bag is 6 slots and you want to go back to town on 2 free slots, set that value to 8.

Dont use ammo bags, just use normal bags, you lose a bit of a bonus, but not enough to worry about.