OK....first of all, there is no true "y" axis on the sub-spindle....only "x" and "z". You can use a virtual "y" by using G12.1 milling interpolation. It sounds like a programming issue to me, or perhaps there is an offset in the "T-DATA" page that might be affecting the tool path in some way. Other than that I think I would need to see the program. You could also send a copy of the program to Citizen, they are pretty good at finding strange things in programs.