Don't if anyone else is having the same problems but there is a bug in SP2 where graphics and charts embedded in a worksheet do not scale to WYSIWYG in PDF.
The Hotfix in the link below looks like it might solve the problem.
I heard about this too... the excel save as pdf feature is kind of limited. If you need to print a sophisticated dashboard or something as pdf, it is better to use one of the pdf printer utilities as they provide finer control and perform better. see more here: http://chandoo.org/wp/2009/06/04/excel-to-pdf/