Hi, Your description is a little confusing and a picture or two would help us. But, reading from that description, are you saying the Ram has two planes of vertical movement? The first is moving the Ram up on the traveling Column, and the second is the Ram cutting head moving within it's slide?
As in the pic, if that is the case, then the cutting head needs to be aligned with the main Ram path.
If that is not the case, can you watch and/or feel the X or Y travel lead screws movng during this process. It may be cross-talk between the axis electronics.