I installed a new hard drive and reinstalled everything. FOr the most part Sonar is running as it should, but when I plug a guitar into my interface, 18i20, I can hear clean guitar with the distorted guitar. I'm using Recabinet, but it does the same thing with Amplitube...
 
It seems like I had this problem years ago, but can't remember how to correct it.

Got it sorted... It was in the Scarlett Mix Control.

MixControl can be confusing at first, and my version is not overly intuitive to access the "router" section which is the #1 used portion for me. With a VST output, often monitoring the DAW rather than a mix is helpful in removing the inputs... is a Catch 22 if you drop unwanted monitors from the mix, since they don't make it to the DAW.

Before I bought the 18i20 I read a lot of reviews and a few of them focused on the mixer saying it can be overwhelming at first. I admit I just stumbled upon the routing preset button. Today was my first day with it so hopefully I've got past the worst part of learning it.