Make sure there is a small break of at least one tenth of a second at each end of the audio on your slides. Don't have the audio hard up against either the slide start or end.
Check the Usage numbers in the Library for your slide audio clips. You may have an audio clip that is used in more than one place. E.g. there may be an object on the slide that has audio attached and this is conflicting with the slide audio. The audio that does not pause would likely be the audio attached to the slide object, not the slide.
Also check whether you are triggering audio via an action. That audio would also not pause just because the slide timeline is paused.