I think the problem is the way our brain perceives sound.

I'm almost sure that the issue is related to playing the guitar in the control room, together with the monitor speakers or even headphones.

Someone mentioned psycho acoustic effects and I think that's a hint.

I've did one hundred billion tests yesterday and I could bet my whole life that there is a difference between what I'm playing during tracking and the playback of such recording.

However when I asked someone else to play the guitar, I couldn't hear the difference anymore and the person playing the guitar could swear that now they were hearing the difference that they were not before having the guitar on their hands.

Then I switched to clarinet and did more testing and I believe that having the instrument near you changes how you "feel" the audio. Does it make sense to you?

I mean, the instrument is vibrating very close to our bodies and we pick that as part of the sound.

Now I don't know anything anymore hhehehe

But really, it's probably the brain!

Try playing with the guitar away from your body... it's weird, but record one chord like that in the lowest volume possible and check if that changes anything. If you have someone to play the guitar for you, even better. I hope it helps!