A couple quick questions:
What does your countdown timer do at the end of the sound file when playing? Does it keep counting after the audio ends? Does the timer stop counting when the audio stops, or does it 'gray' out and after the pause the next file starts playing?
The reason I ask is I've had the exact same problem, but in my case the clock went to gray right at the audio ending yet continued counting for one or two seconds. In my case after troubleshooting (and some dumb luck), I managed to isolate the problem to a bad sound card. I replaced the existing Audioscience sound card with a good ol' Soundblaster card, balanced up the audio using a Henry Matchbox and had not seen the problem after.
I think Howard might be on to something here. I'm not sure he had a "bad card" but a maybe a issue with a driver or how the software buffers it?
With Audioscience they have a large amount of ram on the board which must be filled before the audio begins (or there is not much point to the ram, is there). This prevents skipping but it does take time, not much time, but some time.
A Soundblaster cuts corners on the ram, but it would respond faster. Personally I like the old Santa Cruz cards which handle the overlaps super nice.
I think you might want to try it...