Intonation Problems

[gtrpkr]

I hope someone can help me with a strange intonation problem I'm having with my Legacy Special. I set my intonation today such that the open strings and the strings fretted at the 12th fret are perfectly in tune. Even fretted notes above the 12th fret are in tune. Here's the weird part - fretted notes on every string on the 1st through 7th frets are Sharp. I have a vibrato bridge with 3 springs attached. The neck is fairly flat with very little relief. Any help you can offer will be greatly appreciated.

[Elwood]

The first thing I'd look at are the nut slots. The higher they are, the more the first frets will be sharp.

[DanDoulogos]

I think Elwood is aiming you in the right direction.

[gtrpkr]

Thanks