intonation problem?

Need some clues: Where does it seem most out of tune? Everywhere? Worse at the nut? Worse higher up (e.g., barre chords at six or seventh fret)? Also, you say it "says it is in tune." By tuner or other method?

Just on open chords, picking the E. I use an old tuner.....but i used a friends good one and it was still the same.

Relax your arms and fingers a bit, you are probably pullng everything sharp by pushing too hard on the frets or bending the neck. That's just a guess though. I'd have to hear it to tell you for sure.

It's better to tune a little more flat than too sharp. At least that's what works for me on one of my guitars

If everything sounds in tune higher up the neck -- e.g. playing a barre, then it's probably not a bridge compensation issue. It's more likely a nut problem:

If the nut is cut so the string is a bit too high (off the fingerboard), then for the first couple of frets, the string's notes will be sharp. By top string, I'm assuming you mean the low E. The nut is often not slotted deeply enough for the wound strings. This is a common problem even on new and expensive guitars.

Also, if the nut is not slotted correctly front to back -- or is damaged -- so a string is not properly supported right on the edge facing the fingerboard, then fretted notes will be sharp. However, this will continue to be noticable further up the fretboard.

You may want to take it to a tech to have it checked out.

To check the nut, push the string down at the third fret, then look at where the string crosses the first fret, the string should be so close to the fret that you can not see between them, but it should NOT be touching -- if you tap the string you should hear it click against the fret. If there is space between the fret and the string, then the nut is cut to shallow. If you tap the string and you can not hear the string click against the fret, then the nut is cut too deep.

If the nut is fine, check the intonation with a chromatic tuner, look at your 12th, 7th and 5th fret chromatics, everything should be very nearly spot on. It's best to check these with the guitar laying flat on a craddle so that you aren't bending the string with side finger pressure.