I've had the problem with skipping/pops with known good songs and it turned out to be a flakey IDE cable. I recrimped it and it's been working fine ever since. I've email Rob to buy a new one but he hasn't replied yet. No hurry anyway as I said it's working perfectly so far.

[edit]If you can connect to the serial port when it's skipping you should see loads of HD errors. This is assuming it happens reasonably often.[/edit]

- Trevor