| Most liekly it is because the lower tension of the short scale shows up the most on the low E, and a .090 is pretty low tension even for a long scale.
Try a set with a .105 low E, there are a couple out there for short scales, you can get a 45-105 set of DR Sunbeams and even a 50-107 set of GHS Boomers, the thicker string tightens up the short scale, but then again many like the looser feel with the shorter scale for overall ease.
The other issue may just be the pickups, reviews of that bass mention it as a shortfall, possibly they just don't translate low end well and it isn't as apparent on the higher pitched strings.
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