Maybe I'm just not using the warp correctly? I looked at a couple other levels, and was pretty sure this is how it works. But is this correct:
-A flag warp will only activate if the flag is set, otherwise the room scrolls regularly
-only the direction you want to warp from will matter, in other words, say the room has exits on top, left and right. The warp should activate for the right exit, so you don't have to set anything for the up, and left warps.
Regarding AA's post:
I tried to set the numbers the way the map is actually laid out. So rooms 1 and 2 are next to each other, room 3 is right under 2, and under 1 is another part of the map. You would enter originally from 2 and proceed to 1 (the flag warp in 2 should not yet be active), once activating the shift you end up in 3. 3 is the same room as 2, just the shift tile is removed this way if you try to activate the cutscene again, nothing will happen. Upon leaving 3, you should shift upwards to 2, now with a flag active. If you so choose to move from 2 to 1, the warp should send you down to 3 ( so the shift tile cannot be activated again) and the warp from 3 should send you back up to 2, essentially cutting 1 out entirely. So, you should play like this;
[1] - [2]
[e] - [3]
*enter [2], walk left to [1]* *activate cutscene [1] and shift to [3]* *from [3] warp right Y-1 (normal) [2]* *from [2] either, shift out normally through door, or warp left Y+1 (flagged)* Then 2 and 3 should be connected as if they were 1 and 2.