Okay, lets start at the beginning again!
First off which ECM (Main Computer) are you using? The 92'* or 95'*? Also which Ignition Module are you using? The 92'* or 95'*? This could be your problem, forget about that BCM it'* NOT part of this equation!
My reasoning behind this is simple, The 95'* ECM & Ignition Module may require a DIFFERENT SIGNAL from the VATS system than the 92'* was programed for! There is 15 Different Resistor Codes for the VATS Keys!
It may boil down to replacing the Ignition Cylinder &/or Ignition Switch from the 95'* column!