When using identical sound files across multiple slides, only the first instance plays

I think this is probably the 'Play audio across slides' option.

it's kind of subtle, but if you have the same audio file on consecutive slides, AND this option is set for both of them, then the audio track will play seamlessly as you transition across the slides.

Say, for example, you have the same 3 minute audio track on slides 1 and 2, and you click to transition to slide 2 after one minute:

With this option turned OFF, the audio will stop and restart on slide 2.

With this option turned ON, the audio will continue with the remaining 2 minutes of audio playing with slide 2 visible.

So I suspect this option is turned on, and what you're experiencing is that the audio is just 'playing through' rather than restarting.

I have no idea what the expectations are if the audio track finishes before the transition to slide 2... I suspect that Keynote thinks it's done and therefore doesn't play, which matches what you're saying.