Updated and still have the exact same bizarre behavior.
The presets sound fine outside of Mixcraft. As soon as I try to lay down a track in mixcraft everything gets weird, cutting in and out on most of the complicated lead guitar presets and having what seems like a really nasty not always working noise gate on the distortions (sorry, best I can think of to describe)
Edit: for further clarification, the recording seems to come in just fine in mixcraft, as playing it with no fx and adding other fx to it like the Shred Amp Simulator it sounds fine with no cutting in and out. So the problem does not appear to be with my recording hardware, but with how Mixcraft is processing the Ezmix presets.
The presets I am using that are causing the most severe problems is the Metal Gods vst expansion: http://www.toontrack.com/products.asp?item=169
Outside of Mixcraft, the Ezmix standalone program and the Metal Gods expansion sound perfectly fine. Awesome even.