I have seen this issue reported in other threads, and I have just experienced this problem with Workbench and my Variax 700. I was simply trying to create a new version of one of the Lester models in a drop-D tuning. At first, when I changed the tuning on the low E string to D, I couldn't hear any result. Ah, I realized -- you have to click the Enable button above the tuning chart. That changed the pitch of the low E, but it also introduced a VERY noticeable distortion (like a "bark" at the beginning of the sound) into the A-string -- only the A string, and only when I hit it a little harder than usual with the pick.
Note that this distortion only occurs when the "Enable" button is lit up -- if I click again to disable the alternate tuning feature, the A-string distortion goes away, regardless of how hard I hit the string with my pick. The distortion is clearly tied to the "Enable Alternate Tunings" feature.
Has anyone figured out how to solve this problem??