that sounds as if you're doing several things completely wrong.
For example in any form of cutscene (and all autoruns are effectively cutscenes) it is VERY important that there is only ONE controlling event containing all commands.
ANY try to split up commands between different events is almost guaranteed to cause problems either directly or later in the bughunt.
So the commands you want to trigger have to be in the event that issues the transfer command if on the same map, and if going to a different map then you should start a new cutscene there with a new autorun, but NEVER count on a sequence of commands split over several events.
If you can't redesign yyour cutscene to not need an automated player touch, then post screenshots of that cutscenes controlling events and we'll help you.