It can be a few things, if you plug into an amp is the bass working ok?
Sometimes with new strings the overtones can give the tuner some problems, try playing the harmonics at 12 fret and see if the tuner gives a better response.
Do a rough tune from your 4 string by ear so the tuner is not trying to find a note to far away, so tune E A D G then use the harmonic on the 7th fret E string to tune with the 5th fret harmonic on the low B, if you are not used to doing that then play the note 7th fret E string it's a B an octave above the low B, compare that with the 12 fret harmonic of the B string they should sound the same.
The 5th fret G string is a C so tune the C open string to that, you can also use the 5 fret harmonic on the G string to tune with the 7 fret harmonic on the C string. If your tuner does not have the facility to tune the C string then use the 7th fret harmonic on the C string it's a G note check that with G on your tuner.
See if you have better luck with the tuner with the bass roughly tuned.