Intonation...difficulties.

[Sergio]

mKay. So I decided to whip out my old P-Bass for my band's gig this weekend, and when I played it I noticed it sounded a little out of tune in some spots. I checked to intonation, and everything was fine except for one thing: On the low E (tuned to C in this case), the 12th fret and open string both check out to the same note, but from about frets 3 to 7, each note is a bit sharp.

I don't see any way to adjust for intoation in the middle of the neck, unless it involves the truss rod.

Could it be the string? It is an old set.

Any ideas on what the problem is and/or how to fix it? Thanks.

[Foamy]

The only thing I can think of is that it has to do with the geometry and the tension of the string.
Setting intonation is really just "getting it as close as practical" I think. You can really only tune the string to pitch, and then adjust to also be at pitch at a given fret by adjusting the saddle. Even then, I think that this is just trying to compensate for the geometry and stretching of a string. Perhaps tuning to a C takes that string out of an otherwise acceptable tension range.
Just a guess - but I think that intonation is not perfect anyway. We just try to get things the best they can. I know that some folks intonate other than perfectly at the 12th as well to compensate for playing at higher frets much of the time. Maybe you need to compensate for playing lower.

[SGT. Pepper]

Old strings can cause inaccurate intonation. Try a new set first, then take it from there. If the new set don't work you will probably need a set-up. Enchanter Tim is the best man here to ask about those things.