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Open E string is always flat

I just purchased a player precision bass and noticed that the open e string is always a little flat. I tried adjusting the intonation screw but it still doesn't affect the flatness of the open string. The other open strings are fine though which leads me to believe the problem does not lie at the nut? Does anyone know what it could be?
 
How are you tuning such that you're not tuning the open E string? If you're tuning it to match the A at the 4th fret, and it's flat open, then yes, there's an intonation problem.
 
I forgot to add that it is flat relative to every fretted note on the E string, regardless of changing the intonation screw, my bad

How did you set your intonation? You want to match the 12th fretted vs 12 harmonic. If the 12th harmonic is spot-on(...hopefully the 12th fretted, as well!), it's virtually impossible for the open E not to match. Using a decent tuner?

Compulsory admonishment: set your witness points!

Riis
 
I just purchased a player precision bass and noticed that the open e string is always a little flat. I tried adjusting the intonation screw but it still doesn't affect the flatness of the open string. The other open strings are fine though which leads me to believe the problem does not lie at the nut? Does anyone know what it could be?
I guess your precision bass is not... precise? ba dum tsss :p
You want to match the 12th fretted vs 12 harmonic. If the 12th harmonic is spot-on(...hopefully the 12th fretted, as well!), it's virtually impossible for the open E not to match. Using a decent tuner?
This^^ even the string is dead you will eventually match the two.
 
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This is one more question that proves just how futile it is to diagnose a bass over the internet.

To the OP: Do yourself a favor and have this looked at by a qualified repair person. On the face of it, a bass tuned to pitch may often have problems once you begin to play, fretting notes along the fingerboard.

This? I got nothing.
 
Nut. This sounds (pun intended) like a nut problem. I had a similar problem on my U-bass. When everything was set up with the usual 12th fret harmonic, everything up the neck went flat no matter what I did. It turned out the nut was misplaced. Once the nut was fixed, the intonation was spot on. It could be position of the nut, lack of a good witness point, or any number of other details.

Also: lower the E side of your pickup. The magnet slugs can pull the string out of tune.