Well, it could be fixed if you manually re-wrote every ARE file to have really huge trigger sections.
Basically, press Ctrl-4 sometime during the game with Debug Mode enabled. Then go to some area an d look around. For example, take the area with the diseased followers of amaunator in it. Are you travel to the right from the beginning, there are random encounters with yuan-ti or mummies. If you look closely, you will see this *really thin* bar in the middle of the hallway. You have to step on that to trigger the monsters. If you walk to quickly over it, you miss them.
This is a serious design flaw in these ARE files. Sorry.