Fan17 --
It might be that they can't find a path to the next portal. Perhaps a switch is missing a switchstand somewhere? Perhaps you aren't using Track Markers to guide the AI trainz to the next portal?
I use rule "Central Portal Control" and a series of Track Marks to guide the AI. The combination generally works -- generally but not always. Perhaps consider downloading one of my "Rivercide" sessions to see how the Track Marks are positioned and how CPC is configured.
Loading. There are several "Instant Load" commands on the Download Station. I've had some bad experiences in the past. My recommendation, at this stage until I've done more testing in TRS19, is to get the consist to fully exit the portal, stop at a Track Mark then Instant Load before moving onwards.
Hope this helps,
Phil