"Ghost" lines appearing when creating PDF from Chart

I am using Adobe Acrobat 7.1

When I am in an application (ProM) I can create a flow chart like diagram which has lines that connect the activities (represented by boxes). These lines "go around" any other box that might be in the way when two boxes need to be joined.

When I choose Print to Adobe I can create a PDF successfully.
However these extra lines appear on the pdf that were not there in the original diagram.
They link the boxes in straight lines rather than as described above.
They are faint in comparison to the normal lines.

How do I get rid of them. Any ideas?

Regards,

George