I've noticed the New Industries Nafeys wagons don't carry all resources (doesn't carry fodder, fruits, fish and salt). The normal Nafeys wagons DO carry these resources, but they - and other "New Industries" resources don't render consistently, so it looks like your train is empty despite carrying goods.

Any fixes to this, or suggestions?

Also, really do wish there were alternatives to the Nafeys for some resources - Bauxite / Aluminium being the obvious one - very few vehicles / wagons carry them bar "cheat" vehicles / wagons. (Not that I have a problem with Nafeys / trailerless trucks, I've used them extensively, but sometimes it's nice to use industry or resource specific options)