using the mod to upgrade 1-4 trains, sometimes only 1 cargo wagon gets upgraded

another i notice is that the cargowagons get limited to the cargoamount they originally where (using the better train system mod)

Did you have enough wagons in your supply chest for all of them? If you have an explicit inventory limit set, then it will maintain that limit. If you don't have a limit, then the new one won't have a limit either.

i had more then enough wagons in the supply chest, and no i didnt have a limit set on the wagons, and still the cargowagons are limited to the standard wagon cargoslots