Could be a couple things you should check first...
A. Is the bass intonated? Sometimes when you change strings a new set up and intonation needs to be done again.
B. How high is the just-a-nut set on that side or even all the way across? If itís too high and you have to dramatically press the strings down it could make a sharp note.
The frets are correct Iím sure so there must be a set up issue of some sort. I have also encountered weird harmonic overtones with new strings especially when there is a taper core and a long amount of the core open like DR Longnecks. You can actually get two notes at the same time from the longer part of the taper that hangs over the bridge and the normal part of the string. That can do weird things like make it sound like you have a chorus or even make a note sound sharp or flat.
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