EagleCAD and LPKF S63 Milling machine
I found the source of the problem eventually after some trial and error and also contacting LPKF, so thought I would post an answer as this may well help someone in future.

Basically in the settings for the milling machine, the default setting is to remove a minimal amount of excess copper around pads and traces.  This extends the life of the universal milling bits (40000mm life) and overrides settings used in eagle or Orcad for that matter.

There are a number of options to change this, and they are found in the Insulate menu.  the image below shows this menu


You have 4 types of insulate, shown in the top left, then further sub settings.  the rubout options need you to define a rubout area on another menu, but allows you to remove copper from a large area.  If you are using the 0.2mm Universal Cutter, then I found making 2 passes with this and using a 0.35mm insulate width worked well.  It's important to calibrate the milling depth on a new cutter each time and periodically check it, otherwise I have found it sometimes leaves hair width copper flecks, which can be a real pain locating and removing them.

Hope this aids someone!
Ant