Oddly enough i've found same with my VM4 where D & G strings are slightlly lower. I recently started using D'addarios 45, 65, 80, 100 gauge mainly because mate gave me them when he gave up playing bass and when i changed back to 40-100 gauge again is when i noted what you are saying.
I've also found that using my own Mesa rig its a lot better than the EBS HD360 / Ameg 810 set up in studio. Not sure if its because my Mesa cabs have horns that let the higher frequencies come thru better. I found the original SS Sandbergs were worse than the nickel D'addarios too.
To be fair i have found this with other basses over the years.
Dave