I have a different problem with the E - I play a 5 so when I play the E with as much of my finger as possible, and my finger comes to rest against the low B I get a big thuddy impact sound (from the B string)via the piezo pickup.
But the annoying thing, is that sometimes I don't and it just sounds perfect. But I have no idea what I'm doing differently.
I like the thud sometimes, but I'd like to choose then it happens!