Tell me more, what do you mean exactly with that? Did they make the transitions worse in the XBLA remakes?
One of Rare's little tricks of old was to utilize the cartridge format to swap the tone of notes out on the fly and raise and lower the volume of them to bring hidden background melodies to the fore. The games where this was most noticeable were the Banjo Kazooie franchise, especially the first one wherein the music would change as you approached certain areas in the hub world. It occurred over a very short distance but it was still something of a gradual change, making it feel totally natural.
For some reason, Microsoft appear to have been unable to replicate the same effect on the Xbox, despite the fact that the game is all on the system and so it shouldn't have the same hardware limitations as other modern games.
As a result, The transitions have become instantaneous in places and cossfades in others and it's ever so slightly jarring, though TBH only a big deal if you're actively paying attention to the music. Mind you, given how great it is, you might be.
Worse still is Diddy Kong Racing DS. I had previously assumed that the opening theme was prerecorded but apparently not as the remake completely screwed it up. In the original, the music spontaneously changed instrument every time a new character appeared on screan to match their personality. In the DS version, the entire thing was in one generic and nonspecific tone.
Given that both versions were on cartridge, there is no excuse for that. Sure, they changed some of the characters but the code for the music could still be ported surely. Just change a couple of the instruments and you're good to go.
And don't even get me started on the castle!