Hi Jacky,
Thanks for getting in touch. I just replied to your question on Get Satisfaction, but I'll put down the answer here too
So, this is a bug that affects some users, and I've not managed to track down its cause. I'm inclined to think it's actually an error in the iOS operating system of the iPhone / iPod, which means there is probably very little I can do to stop it, but it could still be a bug in my programming!
I'm sorry though, as it's obviously very annoying

Fortunately there is a very easy work around. You just need to turn the iPhone (or iPod) off, and then back on!
To do this: press and hold down the power button for about five seconds until "Slide to power off" is shown at the top. Slide this over and then wait for the to power down (a few more seconds). Once it is off, press and then release the power button and wait for the to start up again. After this, begin your music as usual and start your run.
Sorry again, and please let me know if these instructions aren't clear, or if you get any more problems.
Thanks, and happy running!
Benjohn