Couldn't fit the full description in the title. The bug is specifically:
Every other screen turns black after Link takes a passage warp between two DMaps that use different palettes.
http://rapidshare.com/files/75723595/BugTest2.qst.html
The test quest build from the default this bug occurs in. Simpy enter the cave from the start. When Link emerges from the passage warp, nothing seems wrong until he moves to another screen. As long as Link doesn't take any non-passage warps, every other screen will turn black when Link enters them. This is independent of the DMap types, as this bug occurs more than once in this test quest.
Windows Build 679, Z3 Movement Disabled.