Looks like this is turning to a bass issue, but I'll give you my opinion. Try what Jimmy says... But also.
I always used flats and the first day on my Jazz changed to Chromes. I also lowered the action as I used to play fretless. As I played I realized the 2007 Amer Deluxe had seriously poor neck / fret issues so I had the local luthier Jewell the frets (fret level and micro polish) and then really cook the setup.
About a month later I modified the bass from E-A-D-G to B-E-A-D. I was able to get the strings back to the setup I wanted. But got in all sorts of trouble with strings not having the same volume levels and just not sounding right.
I thought it might be pickups, my preamp, the fact that 810's don't have as much bottom. I was really scratching my head. I had to figure out what was missing; I asked a lot of questions over on Basses and weeded through the info.
All of my issue was the height of the pole pieces verses the strings. You can make a lot of volume changes and match the strings better by adjusting that stuff. I had a what might have been a couple DB drop on the B and E that I was able to cure by tilting the pickups just a tad. *** add: Also carefull adjustment on the height of the strings at the bridge with the curve of the fingerboard. I don't know what you call it. The E is lower than A and D and G is lower, sort of curving. If you flatten out that curve too much the middle strings will ZING and the outers will be dead in comparison. It was very responsive to the adjustment.
Now I love my setup but it was a lot of hard work and education. A long winded version of Woolysock's response.
GOOD LUCK. BOB