So I've been trying to fix my guitar intonation recently because my B string is awful. However, when guides say that the 12th fret should be the same as the harmonic on that fret, it gets a bit more difficult when that 12th fret harmonic is on the 13th fret instead. Also, the 13th fret itself is the same note as the open note. So is my guitar intonation a whole fret flat? Ive tried fastening the screws but they're as tight as they can go and it's still the 13th fret. I've seen no help anywhere for this issue and I have no idea what to do.
Sounds like your 12th fret is too low, since you need to move up the fretboard to the 13th fret to get the note you should be getting on the 12th, so you need to move the bridge saddle towards the pickups, which is the opposite of what you're doing.
You want to shorten the length of your string, and by tightening the screw you're lengthening it.
Could also be something wrong with your B string, since it sounds like that's the only one you're having trouble with.
The 12th fret is exactly half way down the string. If you are getting the octave and harmonic at 13, then you need to move the saddle forward, towards the pups and neck. Measure the 0-12 fret distance, and then measure 12 fret to saddle. they should be the same, but it sounds like your first measurement will be short, by about 1/2". B saddle on most guitars is farther back than the others, about level with that of the 6th string. Measuring is just a rough guide - it needs doing as you were, using 12th fret harmonic. Some actually check by playing 12 fret note, then fretting on 13, and plucking the string above the fretboard. It's a good guide.
If the other strings are all much more closely in tune (no more than, say, 5-10 cents out) when:
- playing the open string
- sounding the second harmonic
- playing at the 7th and 12th frets
- the action is set roughly equally on all strings
- the strings are all roughly the same height at the 12th fret, and at the bridge
- the neck is not showing noticeable bend
then you've all but ruled out intonation issues, and have to consider that there's a possibility that your B string actually has a manufacturing fault.
I had a similar problem with the E string on my bass when I replaced the strings for a new set of D'Addarios: four of the strings were fine, in that the 2nd harmonic was produced by touching the string over the 12th fret, and also in that pressing the string at the 12th fret produced the same note, but on the E string I had to do it at the 13th fret to get the octave.
Contact the manufacturer of the string, explain the situation, and see what they say. In my case, D'Addario identified a manufacturing fault and replaced it free of charge. The replacement, safe to say, is playing exactly as I'd expect it to play. I've not heard what the nature of the fault was, but in their initial email response said that it could be in the wire core, in the winding, or in the bond between them.