I think this issue has less to do with monitoring and more to do with brain function. I sometimes have this problem, and I sometimes find that it is simply because I am focusing more on my playing than on listening.
For me, it isn't a brain thing at all. Even if it's someone else in the room at the same time, I can still hear the natural guitar.
As soon as the person is playing in another room with headphones, the live and the recorded tones are identical. As soon as they step back into the room, it's off again.
Basically, with the guitar in the room (even worse against my own body), I adjust the sound to make that sound good. As soon as I hit playback, without the natural guitar, it sounds bad.
Doing it oneself, reamping to set ones tones seems like the best solution to me.
I guess the recording, playback, and adjusting that way works too...
Anyhow, setting the guitar tones with the guitar in the room almost always yields small, scratchy, icky guitar tones... especially anything close to high gain.