The first thing you should do whenever an NES hack doesn't work is to open the ROM in a hex editor and check for garbage in the header (most commonly "DiskDude!"). Zero it out. The fact you say it works Nesticle makes this very likely (as Nesticle, at least the most common version, only supports up to mapper 15, thus it ignores byte 7 of the header, the high bits of the mapper, which pretty much every good emulator since then does use)
Zero out that junk.