tuning troubles

Are these still the factory strings, or have you changed them?

Sometimes very old strings won't intonate properly, no matter what you do.

what you describe sounds as if the nut might not be cut deep enough. while this is a common problem with new acoustics, it's far less likely for electrics. but there are always exceptions. as Kent suggests, changing strings is always a good first step. you can check nut height by doing a little "backwards" fretting: fret the third fret, but do it just past the third fret (on the wrong side, toward the bridge) and don't press any more than necessary to just put the string in contact with the top of the third fret. now look at the string's clearance over the first fret. it should be as close to zero as possible without actually touching the first fret. If you can see obvious "air" between the string and the first fret, the string is probably too high at the nut, requiring a deeper cut in the slot. I like my nut height to be low enough that I can't visually tell if the string is touching the first fret or not; so I check by feel, tapping the string lightly right over the first fret. if there is "invisible" clearance, there is a distinct feeling and noise of the string striking the fret. if the string was already touching the fret (nut slot may be too deep), then the feel and sound while tapping will be solid and noiseless, indicating contact.

I recently bought a strat and I am having trouble with the G string in tune with the other strings. the tuner says it is tuned but the d chord sounds out of pitch if I tune it correctly the C chord sounds out of tune. Intonation is correct granted this is a guitar made in mexico. It just seems like I am missing something that is simple Like string trees or inadequate nut depth for the string. anybody with an idea as to what is could be wrong?

First, change strings and see if the problem goes away.