I've had the odd 'rogue' string that seems to need more adjustment to get it in. Usually the E or G for some reason.
With the E (& especially a low B) it might be that your tuner is having difficulty tracking it. Here's an alternative way...
Tune the whole thing up & intonate the G string;
Retune, unplug tuner & plug into amp;
On the D string, play a R5 double stop made of the 12th fret D & 14th fret A on the G. Adjust the D saddle & tuning until that harmonises with the G string;
Rinse & repeat for the A & E strings.
Pete.
+1, That's the way I usually go about it, setting the bass up to itself rather than doing the whole thing with a tuner. I have come across a few basses with fretting inconsistencies that show up by playing double-stops or chords. One thing to remember is to make sure your fretting directly in line and not slightly tweaking the pitch out with a little bending. I've also had a basses that need a little more than usual adjustment, usually on the E or B, string gauge makes a difference in this I've found.