My guess then is that you have a tune a matic type bridge? Stop tail piece with a separate saddle section? If that's the case you are screwed. Just kidding. It might be that one of the saddle posts is drilled in the wrong position. In that case you'll need to plug the post hole and reset the post. An experienced tech could do it if you need.
Are the notes on that string really out of tune with the rest of the strings higher up the neck?
When comparing the difference in pitch values between open note and fretted note at the 12th fret, be sure to use the open string and not the harmonic on the 12th for the first note. If your action is really high on the low E side it might be stretching that next note (comparison note) too sharp when you fret it, hence the inability to get that note flatter.