Here is the recommended portal practices I have found that maintain decent reliability.... Each portal should be dedicated to either emission or absorption. You need to keep a "lead" (i.e. a length of track) that is featureless on both emission and absorption portals. On absorption portals, the length of the lead should be a little longer than your longest train. On emission portals, the lead should be long enough so that the simulation can comfortably assign a driver within the lead for your longest train. Have no track objects or junctions within the lead. Geographically, no track on the route should exceed the coordinates of the portal. That means if it is an eastern portal on your layout, there cannot be any tracks east of the eastern portal. Same applies for all ordinal directions.
It has been posted the SP3 beta devs are working on portals.