Are you able to post up here one of your files? I'd be glad to have a look at it for you if you do so.
You will need to zip the file though, the extension isn't friendly with this forum yet.
Thanks for reply. I have zipped and attached a simple layout. I have included the gerber that shows the problem. Very interested to see if you get the same problem.
I think you are referring the fuducial marks, select Option-->Preferences-->PCB Design, uncheck the "show fuducial marks" and export the outline again.