| Agreed about chromatic tuners being a good idea and verifying reference settings. Also think about a strobe tuner. The moving visual can be very helpful (at least in my opinion).
I find that some tuners sometimes have issues tracking my open E and A strings. But they'll almost always accurately follow their 12'th fret octave harmonics. I tune with harmonics first, then open strings. And note that open strings can read a cent or two sharp for the initial attack.
Also, check the intonation of your bass and the guitars. If your open notes all match up, but everyone tends to drift apart as you all move around your instrument necks, that could be the culprit. There are tons of threads about how to set intonation correctly here, so I won't go into that.
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Jacob
Buddhist #33, Drummers Who Became Bassists #1, Roland #20, Schecter #191
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