OK, your 12 string is in tune on open strings, but sounds rotten when playing a chord. Most probably your problem is due to improper slot depths on the nut.

When you fret the sting between the second and third frets, the string should just clear the first fret. Usually the high strings of the octave courses are seated much too high at the nut. This means that when you fret the pair the high string is stretched more than the low string. Thus the high string plays sharp.