Last night I was fiddling with my Variax after I'd had it set up professionally by my luthier and came across a weird noise artifact when using alternate tunings. This was especially a problem for me as I play mainly in Drop C#.
After trawling the forums and trying the following:
*Adjusting pickup/bridge height to avoid magnetic "pull"
*Trying VDI cable and Regular cable
*Checking HD500x settings
I was at a loss as to why suddenly there was this ghosting of notes amking alt tunings unplayable. I raised a ticket and then happened to message a high profile Variax user who is local to me and on my Facebook. He made mention of ensuring good contact between string/bridge and also a comment about string tension. I replied that I would change the (Already new) strings again just to remove one more possibility.
He then said "Try less string on the machinehead"
This morning when I went to restring, I noticed that my luthier had wound heaps of string onto the machine heads.
I use this method of stringing a guitar (Look at the "Vintage tuners" section a bit down the page), which means you have very few winds (Generally less than 2) on the machinehead. When you pass the string under itself, it "self-locks" and doesn't require a bunch of winds to "grip" the machinehead.
Tuned up and viola, no more ghost notes!
I rang my luthier and had a chat to him about it, and he said that the reason he winds so much is to ensure the strings pass on vibration through the headstock. In my opinion, this appears to be what the problem is. The guitar is resonating with the true frequency of the strings, and this is why you hear the ghost notes.
I'm not here to get into an argument about the best way to string a guitar, but in 24 years I have tried many, many different mays to wind strings, and after I got this guide in my PRS case, I use it for 14 out of 16 of my guitars, and the exceptions are my two classicals. TL;DR: Try less winds around your machineheads.