Hey guys, first off I have a Squier Stratocaster which has horrible intonation on the high E, B, and G strings. When the strings are tuned, at the 12th fret they all sound flatter than they're supposed to. I tried adjusting the intonation by moving the saddle closer to the neck, but even when they're moved all the way up, the 12th fret still sounds flat. Is there anything else I can do to fix my intonation? Am I doing something wrong? Is my guitar a total piece of ****? Thanks.
The problem is probably in the neck, you should check the truss rod setting.
Hell is empty. All the devils are here. - William Shakespeare
Well my neck looks fine. It seems just a bit concave (or convex, whichever one means the neck is bending away from the strings) which I think its supposed to be. How would I fix the truss rod setting?
It's NOTHING to do with the truss rod, don't touch it....you only adjust intonation at the saddles.
Actually called Mark!

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Definitely not the truss rod. It is possible the bridge placement is a little off. This happens sometimes on budget guitars (and once in a great while on more expensive ones.) Also sometimes they have a little too much play in them (tolerances aren't good.) Take it to a tech and get a set up.