What motherboard/Firewire card do you have?
There was a post related to this the other day with an external HD, like I told him, I had the same problem with my external HD (essentially what an ipod is to the computer) when I have my Iwill KK266-R (KT133A) and a cheap VIA chip based firewire card. Also introduced data dropouts when capturing DV. Same drive, same DV device, no problems with this nForce2 board with built in firewire.
Solution suggestions...copy smaller amounts of mp3s at a time. Replace firewire card with one of a different chipset. If you have another computer in the household try the firewire card in there (especially if it's a different motherboard chipset - that same firewire card I have works fine for DV capture in an old intel LX chipset motherboard).
I tried playing with PCI latency timing thinking the tricks that helped with SB Live! cards crackling on VIA boards might fix it, but it didn't make any difference for me. Not saying it won't help, just wouldn't invest a lot of hope in fixing it that way if you have a VIA based motherboard. Loved my VIA stuff otherwise, just that firewire problem 🙁