My guitar is tuned and I have also adjusted intonation.

However, my guitar sounds off tune when I play A-chord. The 2nd and 3rd string actually create a ringing sound and if I tune the 2nd string to adjust to A-chord, it now sounds OK. But, now the D chord is off.

I think it might the Schecter stock pickups / intonation / truss rod issue.

What could be the problem?
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Yeah, check your intonation.

But the thing is, guitar will never sound perfectly in tune. It's a bit flawed design and that's just the way it is. This is why "true tempered" guitars exist. They fix the tuning issues with normal guitars.

This is how true tempered frets look like:

Another problem is that there's a major third between the G and B strings. And a major third that sounds perfectly in tune is actually a bit flat when compared to the equal temperament major third. So you shouldn't use a major third to tune your strings. If the major third sounds perfectly in tune, everything else will sound off. That's just how it is. We use 12 tone equal temperament to make the instrument sound good in all keys. That makes thirds slightly out of tune, but it sounds good enough and you really won't notice that when you listen to music. But yeah, this is the reason why you shouldn't really use thirds to tune your guitar. Octaves and unisons are the best intervals to use, followed by fifths and fourths.

You need to make some compromises. Even a perfectly intonated guitar will not sound perfectly in tune because as I said, that would require true tempered frets. The guitar is a bit flawed design. The frets are a bit misplaced.
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Well since nobody is going to run out and buy a new neck with the squiggly frets, I will just agree with the rest of the responses. Check intonation, and use a good tuner or it's not going to come out right.