Chances are, the game is hardwired to move link to a specific screen that is hooked up to the warp room. The warps won't work because it isn't hooked up correctly. A simple workaround to this is to not move any of the warp rooms in the rom, or not to use them at all.
I am looking for someone to help solve a problem which has recently been encountered on my romhack of The Legend of Zelda for the NES, involving the warp rooms. The game runs perfectly until you enter the warp room and use one of the staircases to go to a different location. When the player interacts with the staircases the game crashes. This may be caused by the player not yet possessing the power bracelet, or the new rooms that have the warp subroom aren't configured to be warped to. My guess is that the code for the destinations of each individual warp room needs to be rewritten. If anyone knows how to fix this problem, please reply below how this can possibly be fixed. This issue is critical, as the warp points are now necessary to enter dungeons L4Q1, L8Q1, L4Q2, and L9Q2 (Level x, quest y).
Thanks in advance!