treelegs,
My friend had a very similar issue with his DAW.
It was a Dell with a Digidesign factory 003 (firewire) connected to a texus instruments (I think) PCI firewire card. We had similar audio pops/clicks to what you describe, especially when running Reason and Live. What's worse though, is that we often had times when the screen would go black for a second before briefly returing, only to repeat back to black (not to mention whatever audio was playing at this point glitched then froze).
Like you, it got progressively worse over time, however this does sometimes vary. Dell nor Digidesign could come up with an answer so eventually we wrote off the machine (we still have it though) and started using a Dell XPS laptop instead.
After a lot of troubleshooting though, I do believe it was something to do with the firewire card (or indeed it's way of interfacing with the motherboard). It wasn't a software issue because we too reinstalled the OS, and nor was it the 003 because it worked fine when connected to another machine. Essentially, the system temporarily halted with a black screen and frozen audio, almost as if the CPU had received some sort of hardware interrupt (assumably from the firewire card?). Dell have a very extensive hardware test partition factory-installed on the hard drives (we had 2 on RAID 1) - we ran all the tests (bar the extended hard drive ones which would have taken days to complete) and nothing failed. We never got round to changing the firewire card but I think that may well have been it since it was a 3rd party device and Dell's tests didn't cover it.
It has been a while since we had this and I've definitely forgotten a few things - I'll add more detail if I remember it!
I hope this helps you
