How are you hooking up the interface? If you are using it as an interface, you should be using the ASIO drivers.
If the problem is with pre-recorded tracks, then those should be imported into your target DAW. Monitors should be going through the Zoom, not the PC. If you are playing through the Zoom, then the output control just needs to be reset.
If you are recording from the Zoom to your DAW, then you are not using it as intended. Probably the worse way to transfer your music from the Zoom to your computer.
If the above doesn't help, give us a little more information on what you are doing to cause the issue.
Hmmm.... now that I'm re-reading your post, I'll go back to see if I'm using the right driver. I'm pretty sure Zoom didnt' give an option for windows, in other words I think there was only one driver available for windows and one for mac, but I could be wrong on that. Let me check that out.
To answer your other questions, in Cubase I've selected the Zoom ASIO driver. I'm only using the zoom as an interface, so I'm plugging my guitar, vocal mic, etc into it, then going straight into the computer via the zoom's usb out and I'm recording on the computer. The problem is happening both with pre-recorded tracks as well as new tracks, and with a test mp3 I created from a test song I recorded yesterday with it. Monitors are going through the zoom. I'm hearing the break up both in my monitors and in my headset, which is also plugged into the zoom. Keep in mind, I'm not hearing the break up when using the focusrite as an interface, just the zoom.
My set up is pretty simple, so there's not much else to describe, except that I went through and adjusted all the record and playback levels in windows control panel and that had zero effect on anything.
The only thing I can think of that I haven't tried yet is the version of Cubase I'm using is LE 5. The driver that came with my zoom and that I downloaded from zoom are for the current version of LE, which I think is 6.
Could that be causing an issue? Again, I used 5 on my last pc and I'm pretty sure the driver was alos for 6 and I wasn't having a problem (though I could be wrong on that, it was a year ago that I installed it so they may have updated the driver).
I think I'll first check to make sure there isn't a separate windows driver that I missed, and then I'll try installing LE 6 to see if that solves the problem.
Thanks all! I'll try to post a follow up to let you know my progress.