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The tuner in Guitar Rig would work.
Then you just adjust string length until you're getting within a couple cents of E with both an open string, and when fingering the 12th fret. No need to check the harmonic.
Edit: Additional things to note...
Try to play each note the same way when doing intonation. The same pressure on the fretboard, the same amount of plucking force, etc. And it should be about how you would play it normally.
Because where you press the string down within a fret, how hard you press down on it, whether you're bending the string one way or another when pressing it down, and how much, all have a slight effect on the resulting note. You can actually measure this with a tuner that displays cents. Press the string down as lightly as you can while still getting it to make the proper note, and you'll have a note that's a cent or two lower than if you push down harder on the string, because when you push down harder, the string is stretched slightly more over the fret, creating a slightly more taut string which sounds slightly sharper.
Also try to be consistent with how much pressure you're applying and how hard you're striking the strings when playing, sometimes--especially when a given position is giving us trouble--we may push down harder on a fret trying to make sure we get it right, which actually distorts the note slightly and may make the issue worse.
Not to rule out other things too, but the attack on the string might screw up the initial detection - either as a miss or as too sharp. If you have a lot of attack noise, it could be registering that instead of the true note.
I don't really rely much on the note detection anymore. It can be wrong in places simply because the note tracks are just tiny fractions out of sync. I mostly use it for sightreading and working on my headcount for songs.
Otherwise I mostly just use RS for easy access to songs I like to play, so I have something to play along with or for certain amp/effect sims.
I've had 70%'s in songs that sounded 100% dead on and if I had worked to get them to 100%, they'd sound off. I know you can dial in some settings in the game for this and my situation also isn't the 'standard' (I'm using an audio interface and not a THIRD realtone cable)
The old phrase 'if it sounds good, it is good' generally applies.
Had the game give me 99% on a playthrough of something last night and I just went "Well I dunno where it thinks I messed up, but it's wrong" lol
I've even had it work the opposite way, I've got some trouble playing fast a lot of the time so some songs I play at half the notes (16ths to 8ths mostly) and I've had them be like "Nope that's perfect"
I mean it wasn't
Sometimes it sounds okay for fun noodling around but it's definitely not 'correct'
The Ducks redux guitarcade game was great for showing me my intonation was out.
Is it just the 6th string that gives you hassle?
The arrow pointing to the left suggest it thinks the not is flat. so that's a good sign that you're not just squeezing the note out of tune.
So, I'd guess that it's a setup issue. - If it's just the sixth string I'd check the saddle height on it. The low saddle on my High E used to cause the string to settle against the higher frets and deaden whenever I fretted much beyond the 12 fret. My truss rod needs a touch of adjustment too but I've just raised the E saddle for the time being until I try my next set of lighter guage strings. they'll most likely relax the neck a bit with similar results on the action.
All my guitars were poorly set up before I started with Rocksmith. Learning how to set them up has cured a lot of these issues. These days rocksmith often overlooks my mistakes.