Door standards

[cobra4237]

Hello all.  I was hoping someone could help me or has run into this problem.  When I adjust the door standards and set the Stile and Rail length cutter depth to .45 and my tenon length to 0 the rails on the upper cabinet doors are perfect but the lower cabinet doors are an inch longer than they need to be.  If I bring the S&R cutter depth lower, the upper doors start to change and the lowers adjust themselves.  I'm pulling my hair out.  Help!!!!