Pops appear after mixdown - hardware problem?

[feilgrep]

Having been a Vista user for a week now, I've finally got my 828mk2 firewire up and running the way it used to on my now retired XP-laptop. Playback is fine, recording is fine, cuemix works good. I'm using the 1394 port. The computer is a Dell inspiron 1525. MOTU driver version is 3.6.8.1328.

When I record audio using Cubase SX2 the recording plays back fine. No pops, no clicks, just clean audio. But when I mix it down (i.e. mixing several tracks into one stereo interleaved file), I get pops. Not a lot of them - one or two in a three minute audio clip or so, but enough to ruin my evening. This phenomenon occurs regardless of plugins applied and samplerates/bit resolution used or mixed down to.
I tried messing around with buffer sizes ("Samples per buffer"); really low settings made it worse, but medium and higher settings didn't solve the problem. I experienced the exact same thing using my XPsp2 laptop as I do now with my current Vista laptop.

My question: Anyone have opinions to whether this is a hardware or a software (Cubase, WinXP/Vista32) problem?

Thanks!