If I'm reading correctly, you're saying that you used the rule as an Auto-Import rule, and it works correctly for Name. But you also have a Media Sub Type rule that just sets the name to Trailer but that rule does not fire/work?
Reading further into this... Since you can't assign two fields in one rule (bummer, and makes simple things harder), you'd probably want the same basic rule twice, once to use for cleaning Name, once for use in setting Media Sub Type.
So, you could use something like:
Name: ifelse(Regex([Name], /#^(.+?)( \(.+ Trailer\))?$#/), [R1])
Media Sub Type: ifelse(Regex([Name], /#^(.+?)( \(.+ Trailer\))?$#/), Trailer)