I would change the strings to eliminate that variable.
The most likely culprit if I were to guess is the b string is too high at the nut.
when you fret it at 3 and tune, you are adding tension to the string as you push it down from the open position.
This may result in the open string then being flat.
If the rest of them are ok and intonation is not problematic, you nut slot is positioned correctly.
The distance from the front edge of the nut to the first fret must be correct (as well as all the frets /fret slots).
This is from the Graphtec nut installation.
I use this but eyeball the heights rather than measure, for all strings as sometimes the nut slots do not follow the fret board radius accurately.
I leave my lo e and A strings slightly higher to compensate for my ham fisted chord picking/strumming or they buzz, esp. at 25 1/2" scale.
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