Not So Pretty URL IIS6

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Ok, I am running Concrete 5.4.2 on IIS6.

My webhost has ISAPI Rewrite 3, so I am able to use .htaccess.

My problems start when I enable pretty URLs. It breaks the layout in Firefox 6 and IE9 not but Chrome. Additionally I lose the edit bar at the top of all pages. In the dashboard most of the function don't work, specifically in the Site Map section it shows "page not found" for all the pages.

Anyone have some thoughts?

Thanks