This problem occurs when your printer is set to a resolution higher than 300dpi. Intersection Magic is still printing to some internal coordinates that reflect 300dpi.
Versions prior to 6.608 assumed a coordinate system that was 300dpi X and Y. As a result, newer high res printers cause the diagram to appear smaller. This problem originated sometime after 5.511 when the same assumption was not made. (intended enhancement)
The best solution is to upgrade to 6.609. This entirely fixes the problem. The first workaround is to simply tell Intersection Magic to print the diagram twice as large. (set the width to 36cm) The other workaround is to change your printer driver settings to print at 300dpi instead of 600dpi. This will work, but won’t be remembered session to session.