Presenter 10 Changes Colors to slides in PowerPoint Deck upon Publication

Using Presenter 10 with PowerPoint 2007.  When I preview PowerPoint slides in Presenter all looks great, color and builds are fine.  When I publish the slides as SWF and/or HTML the fill colors and background colors change on many of my slides.  The change is made to the published material as well as the original PowerPoint slides.  Some of the changes made are so bad that the presentation becomes not usable for the audience.  I go through the process of changing the colors back to the original, re-synching the slide since when you ungroup to redo the colors you loose the animations.  Some of animations are very complex so this takes much time and is incredibly frustrating.
My questions are as follows:
1. Has anyone run into Presenter 10 changing fill and background colors to published material and their slide deck?
2. What is the fix or work-around that you used to overcome.
Thank you for your help.

Hi Monica,
Please package the presentation and mail me so that i can have a better look..
mail id:[email protected]
Thanks
Sidhartha

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