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New shortscale player, wondering about unfocused E string

I tried some rounds on it just now, and the problem persists! It's so odd, the strings sounds unfocused and anemic even when it's not being fretted, even with different strings.

Show us a photo of the strings going over the bridge saddles from the side...;-)
Have you tried lowering your pickup height away from the strings? Just a fraction of an inch can make a difference if it's too close.