Art, Brian, Someone!!!
I have read every post about missing steps in the "Y" axis and applied all of the fixes i could understand.  When configuring motors the "Y" AXIS runs fine (no skips).  I have changed motors from one drive to other to see if it was the motor - no difference.  Changed out cables - no help.  
I have shut velocity and acceleration down to minimums or set to maximums and still get skips.  Changing to Sherline mode did not help.
I even pulled the lead screw our of the "Y" axis to determine if it was screwed up or blocked.  Looks okay.  Like I said - "Y" works fine when in the motor tuning mode.
I have determined in MIDI when I type in same distances for "X" and "Y" ex: G0x4 y4 - Y4 "Y" does not skip steps.  If I type in different  distances - ex: G0x4 y2 - "y" skips steps.  It isn't compensating for the differences.  The machine coordinates are wrong for "y" after the exercise.
Any suggestions will be appreciated.
Thanks
Bob