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Losing my mind tuning a five string

The easiest way to set your intonation is to tune the 12th fret harmonic to be exactly in tune, using an electronic tuner. Then push down precisely on where the 12th fret would be and if it's flat, move the bridge saddle forwards, then use the same method again and it should be closer. Keep doing this until it is in tune.

If it's sharp do the same, but move the bridge saddle backwards (ie. away from the neck). It can help slackening the string off when moving the saddle backwards.

There are more in depth guides and probably better ways, but in a nutshell that's how you do it. You'll certainly get a better result if your intonation is way out, though on this occasion it appears to have been your tuner. I recommend a Boss TU-2 or better for picking up the low B.
 
I got all the guide on intonation I need from my warwick owner's manual.

If the 12th fretted note is sharper than the 12th fret harmonic, you need to make the string longer. If it's flat, you need to make it shorter

(of course i'm pretty new to this set up sort of stuff so maybe there are other issues at play)
 
Some tuners are very sensitive and you can try rolling your volume back a little to increase accuracy. Sometimes certain bass guitars throw a hotter signal and this will throw the meter off on your tuner.

Try it. It even works on hot guitars..
 
BTW, I ALWAYS use the 12th fret harmonic when using an electronic tuner. It's easier for the tuner to count the vibrations (like having a higher sampling rate) when there's more of them. Your properly (standard) tuned open A string is 55 cycles per second, but the 12th fret harmonic is always going to be exactly twice that at 110 Hz. So the tuner has more chance of counting the higher sample right than the lower one. Go ahead and use the harmonic to tune.

John