You can solve this by adding this to your user.config:
<add key="UseTransferRequestForUrlReWriting" value="false"/>
However it is more ideal to use an integrated app pool.
I recently changed the url rewriter module to use Ser.ver.TransferRequest instead of Context.RewritePath but kept the old implementation using this config setting in case it caused anyone any problems.
The reason for the change is because with RewritePath, what happens is that the IIS log only sees the real url, ie it logs all cms pages as /Default.aspx?pageid=x rather than logging the friendly url, whereas with Server.TransferRequest (which was a new feature as of ASP.NET 3.5), it will log the friendly url in the IIS log.
Given the new European cookie laws and the growing use of do not track and private browsing sessions which aren't tracked by google analytics, its growing important again to be able to do server log analysis as an alternate means of measuring site traffic. I recently installed SmarterStats on my server and discovered this problem that the reports were not showing the friendly urls because the IIS logs did not have them. So I made this change to help going forward so that the IIS logs will have more useful information.