I don't know if this is a TS12 issue (I hope not!), but in TS2010 I made a session with two TM acting as portals and it worked smoothly.
In that session, the player drives a railcar which meets two trains, a freight train and a passenger train. The opposing trains were generated by two different portals (each one of them generating one of 8 possible trains, with different consists and orders, just to make the session playable again and again by varying the train consists and the stations where the meets take place).
I just checked the session: I used an "Un-portal" rule for every portal emitting trains (two portals, two rules).
A single "Un-portal" rule should be able to manage several trackmarks used as portals, but if I remember correctly I used two of them because of some issue, though I do not remember if I also saw single locomotives coming out like you.
I'll ask to a friend of mine who helped developing that sessions, but I think he will answer no earlier than tomorrow.