Its seems that on my tube amps when i distort them the distortion is really shaky and doesnt settle. almost like there is the fundamental of the note and then another pitch on top of it that goes in and out of tune ever so slightly while i play them
This is only when i play single notes though on the G string to the E string (high one). ...
When the noise is only on a single string, and only over a span of a few frets, it makes me tend to question the guitar.
But let's assume the amp/distortion is the problem...
You may want to try less distortion. Every pitch that's note a pure sine wave has overtones. That equates to a fundamental and one or more (usually many) multiples of the fundamental frequency. The lower harmonics are musically related, but the upper harmonics are not. Further, some of the natural harmonics produce a pitch which is out of tune with the same note in the equal temperament system.
I'm mainly thinking of the 5th harmonic, which is a major third but is 14 cents flat of equal temperament.
Further, more than one tone (and this is true of a fundamental and its harmonics, even for a single note) applied to a non-linear device/amplifier outputs the original tones plus the sum and difference of every two of the tones present in the original signal. This is intermodulation distortion, and creates notes both above and below the original pitches.
Intermod distortion is part of why distorted notes/chords sound like they have more "beef" but can result in a lot of new tones which are discordant with the original note. A good way to hear the effect of intermod distortion is to play/release an oblique bend (say, play/hold 12th fret high E, bend 12th fret B string up a whole step) up around the 12th fret. Under heavy distoriton, you'll hear intermodulation as a low subharmonic that seems to go up in pitch as you release the bend. This is a difference frequency you're hearing.
There's other possible causes, like power supply ripple being amplified by a stage that's distorting heavily. But rather than try to second-guess the quality of the amp you have, there's 2 general solutions:
1. Reduce the distortion.
2. Try a different amp.
If it's not the guitar, you'll probably find amps that make the weird sound less than others, if at all. I can't say I've ever had an amp make the sound you describe, though my ears have gotten more acute and I'm starting to get very frustrated with the out-of-tuneness of equal temperament and the guitar.
It
almost makes me want to tune to an open chord and play slide instead. I did once know a jazz guitarist who built himself a fretless guitar, largely for soloing and (I assume) to be able to finger every note in tune.