Why whole E string sounds flat.

What kind of bass?

What solutions did you try with the nut?

Did you check witness points?

Pickup(s) close to the strings?

 

If the string sounds flat when you go up the string, it means the E saddle probably is too far back on the bridge, bring it closer to the neck.

 

Did you check neck relief?

 

What does your string wind look like?

 

The open note sound flat? Obvious question but are you sure it's tuned properly?

Do you know how to intonate the bridge? If not there are tutorials on the 'net.

A witness point is created by pressing down on the string just in front of the saddle and on the fingerboard side of the nut. It eliminates any arching of the strings at those locations.

 

This may sound obvious, but if your OPEN E string is flat, you need to tune it to pitch.

 

Not to be picky but -- does it _sound_ flat (compared to what?) or is it flat?
What are you using for a tuning reference?

 

Turn the tuner until the open E isn't flat.

 

Do you mean flat, as in pitch, or just dull, no sustain, etc?

 

This is my suspicion as well. I don't think we're talking pitch here, folks. I think we're talking tone.

 

That would make more sense.

 

Exactly precisely this.
I picked up a used Precision sight unseen many years ago, and the E string was lifeless. Drove me crazy for the entirety of five whole minutes until I simply unwound it, trimmed it slightly (too many wraps) and strung it back up.
Not only were there too many wraps around the string post but it was also twisted. Seems like the seller swapped out strings in a hurry before shipping (he gave me the choice of rounds or flats.)
Anyhow, just buy new strings and see if that fixes your problem.

 

If it's a new string, I'd say something is wrong with it. Get a new E string on there and report back.

EDIT: Never mind, I see you've already done that.

 

Did you uh bend the string a bit before cutting it to length?

 

Sometimes when you have tried everything in a logical manner, you have to come to the conclusion you have a piece of wood that just doesn't want to be a guitar. Not every tree gives up musical wood.