I had what sounds like the exact same problem. I'm running a firebox with an amd laptop. I spent several months troubleshooting and finally came up with a fix.
For me, it was a driver issue. What I suggest is doing a format and a fresh install of windows xp (not media edition). Make sure it's not bundled with software, just an oem version. Then install only what is totally needed to use the firebox. Basically, the firebox drivers and cubase. Don't update any drivers, don't install video drivers/mouse drivers/antivirus etc. Then test out the system. If it's still skipping, do some optimizations (again, not installing drivers etc, but doing windows optimizations). Test again. If it's a driver problem, you should find your system stable (or at least more so). Do a system backup at this point. Then slowly install each driver you want to run on your system. Test the system between EVERY driver install. Then install necessary programs again testing between every install. If you're problem was like mine, you'll find at least one driver/program that causes the system to skip.
For me it was an updated mouse driver, and norton antivirus.
One last possibility is your firewire chipset. Make sure its not a NEC chipset, as they don't work very well with fireboxs.
Hope this helps, best of luck.