Biesse help?

[mrwoodworks]

I have a Biesse A3.4FT 2007 model. This machine has a drill block mounted on the main Z axis (ball screw) and then the spindle motor is mounted on an air cylinder/linear bearing - all this is one assembly. When processing sheet stock and material under 3" there is usually no issues. However, when I wish to machine thicker material (the machine has a clearance rating of 6"), the spindle motor does not extend all the way down the axis. It goes part of the way and then the drill bank assembly extends the rest of the way. The drill block is then too low to clear the material if I am cutting deep pockets or profiles.
I'm not sure if this is a post processor situation or if it is something within the controller software (NC600). Any information would be helpful.
Thanks