Heavy Low E-String Sound ASAT BluesBoy

What size are your strings? Could it be that the low E is extra heavy? Ernie Ball has Heavy Bottom sets that have a 52 as the low E, rather than a 46. Did you change the strings? Perhaps the adjustable pole piece on the pickup(s) is adjusted too high or something? I'm just taking some WAG's about it. I have a Les Paul with a Seth Lover HB in the neck and I love the sound of it. I run 10-46's on it, like most of my other electrics.

Assuming you are using standard tuning ? You may want to check pickup height on the bass side - It may be too high. If you depress the string on the highest fret, you should have about 1/8 - 3/16" between the bottom of the string & pickup. Hope that helps!