That's fine about the zeros. That's what it's supposed to be when it's all extracted like that in a ISO/WAV/CUE format. If it was in a BIN/CUE format, the CUE sheet would look different.
Okay, so I suppose you could try changing the track's length to match the one that was working. If you have to do that, then it wouldn't be a bad idea to add a 15 second fade out like Paranoia Dragon said. I would just use Audacity to edit the track. It's just the menu music anyway, not a big deal, haha.
Btw, what are you using to test it? Ootake or some other emulator? You're not burning CD-Rs right?