I have been having exactly the same problem, and I'm not the only one (according to the iLounge forums known bug list for iPod Classic).
I have noticed that the problem occurs more frequently on tracks ripped at a higher bit-rate (256kbps or Apple Lossless) than on tracks recorded at 128kbps.
I've taken my iPod back once and got a replacement which, if anything, was slightly worse. I reckon that in an album (70 mins) recorded with Apple Lossless, I get on average 2 pauses. Sometimes it's better, sometimes worse, and it never occurs in the same place twice.
I imagine it's probably some kind of buffering issue, and I'd be very surprised if Apple don't know all about it. To date, they seem unable to fix it with software updates (I'm on 1.0.3), so perhaps it's a hardware fault, in which case we might have to wait until the 7G iPod!
I'm going to take my iPod back again after Christmas and keep doing so until somebody takes notice.