What was the old Arbortext version you were using? From memory, in Arbortext 6.0 they changed from Larson CGM engine to the ISODRAW (IsoView) engine for CGM. This may account for the difference in CGM output.
You will probably need to open a support ticket with PTC to get assistance on this. Ideally you could supply them a PDF from your old system and a matching PDF from the new system so they can see the difference for themselves.