I can't get them to work at all. Been awhile since I used them, but I don't think i'm missing anything...
So the rooms in question;
are both in Dmap 21, lv124.
Room 1 has the boss flag, an enemy, and enemies->secrets.
Room 2 has the boss flag, a trigger, and enemies->secrets.(with secret flag 16 to cancel pit warps)
After defeating the enemy in room 1, enemies->secrets activates, but in room 2 enemies->secrets does not trigger.
I'm pretty sure sure this is set up correctly. I don't see why it doesn't work though...unless i'm missing something stupid...
EDIT: I just double checked this setup. Everything looks fine. Freedom, if this is indeed correct you might want to move it to open bugs forum.