So this is through the iPhone app then? Audio playback has been fraught with problems recently, which is why I have been working on a new audio engine to replace the current one being used. I wrote about the issue here, although I started over from scratch on September 1st with a new audio engine (#5 for those keeping count) which will hopefully be approved by Apple for beta testing in the next day or two.
That said, this particular problem sounds like it might have something to do with the Bluetooth speaker (assuming you’re using one). Some Bluetooth speakers go to “sleep” if there’s no audio for awhile, and they drop out the first little bit of audio that is played. Strum Machine attempts to work around this by playing a very quiet bit of audio, then starting the real playback after a short delay. But I’m not sure it’s 100% effective.