If memory serves me right SR had the ability to switch tunes without stopping the music as whole. Some instruments would simply expire and new ones would replace them. This wasn't always the case, but still... It's easy to reproduce in the very first tunnel once the intro sequence is over - the music changes as Raziel approaches the first teleport platform. I remember it well because due to a bug in my SH4 there was a time the game would freeze at this very moment.
As for the instruments being too short - I might have an idea. I'll get back to you soon