OK so i have a 79 les paul and my b string won't stay in tune above like the 9th fret. i understand how intonation works but if i check the open string against the 12th fret harmonic, they register the same (both in tune). could this still have something to do with my intonation or maybe a whole other problem?
I don't know what the problem is, it sounds a little weard to me. Maybe see a good guitar tech/luthier and have them tak a look.
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Is this a new problem (how long yea had the guitar, are these new strings, old strings) if so it may be a dodgey string or as the previous post new strrings required.
Check the intonation whilst fretting the 12th instead of the intonation. If the action is too high, The 12th harmonic will register differently to the actual 12th fret.
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I'd start by double checking neck relief, doesn't sound like it's going to be that based on it only being 1 string, it's not likely my second check:

check the open string, fretted 12th, and harmonic 12th, they should all read (roughly) the same note, if they don't then you need to adjust the intonation at your bridge.
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