When the data file in the Illustrator 9 format is opened using the Illustrator CS6 and later editions, the name of all layers are changed to 'layers'. The Cutting Master 4 cannot to recognize registration mark because the name of layer for the registration mark is also changed.
The cause of this phenomenon is not the Cutting Master 4. It is issue of the Illustrator CS6 and later editions. It occurs when the illustrator 9 format data is opened by the Illustrator CS6 and later editions.