I am using this mod with one of the Bobs mods that adds additional turret tiers. the higher levels allow second and third ammo slots (meaning it can hold 400-600 bullets) and as soon as the first ammo slot is used, it will throw up an "empty" warning even though there are another 200-400 more bullets in the turret

Please check your settings. If the multi slot mode is set to "individually", this is the intended behaviour. To add up the slots, use mode "added".

If it is set to "added" and still behaves this way, report back and I'll start the error hunt :)