The notes i am hearing are octave sounding lower and out of tune with the root note, it decays before the root note, and more noticeable the harder you dig into the note. I will try to upload a clip as soon as i can. Thanks for the reply’s
What guitar are you using?
I just built a 5F6A that does this to a certain extent, as do some of my other vintage-style amps. And by "this", I mean the
exact phenomenon you describe above. I was a bit worried that I'd done something wrong, but then I tried playing some overdriven leads with the same guitar on my trusty C-30, and low and behold, ghost notes! (Why had I never before noticed this?) Then I tried a few more vintage-style amps, and some did and some didn't. Then I tried experimenting with pickups: Les Paul humbucker neck pickups = annoying out-of-tune ghost notes on many amps when overdriven. Single coils = almost never, occasionally on a very hot neck pickup.
I spent some time tracking down possible causes. (I tried grid-stoppers, messed with grounding, tried to track down oscillations, etc. to no avail.) Then I searched for this phenomenon on the guitar forums. It's apparently common, especially among Les Paul players who play overdriven leads on the neck PU. I came to the conclusion that the cause is the "vintage" power filtering on some amps that were never designed to handle the thick, powerful tone that comes from a Les Paul humbucker. You can beef up the power filtering, but that changes the tone of the amp, and I chose to leave my 5F6A stock. Interestingly my Les Paul is the main culprit, and I can successfully use my 335 on most of my Tweed amps w/out ghost notes.
So my solution is to match the guitar to the amp. I'd never sacrifice the magical sound of a Tele through a great tweed just so I can play overdriven Les Paul leads through the same amp. Your problem may be something completely different (I didn't read the entire thread), but I can say that your description sounds exactly like what I'm hearing.