Hope this helps someone. After upgrading to IE9 and SQL Server 2008 R2 CU7, I found that I couldn't access Report Manager anymore. I found that even though I was in the BUILTIN\Administrators group, that I had to specifically add myself to the Content Managers role in Reporting Services for the root folder of Report Manager. (I have no idea why as it used to work ok) NOTE: I had to do this with UAC turned off, otherwise, Site Settings, etc. were not visible. Remember to turn UAC back on if you did this temporarily.
But the bigger issue was that Report Builder 3.0 would not launch, even after I got the button back on the screen. The message was that I needed to install the .NET Framework 3.5, even though I already had .NET Framework 4.0 installed. Nothing I did seemed to fix the problem.
In the end, the issue is that Report Builder 3.0 will not launch from Report Manager in IE9 unless you enable Compatibility Mode (normally used for older web sites that don't render properly in IE9) for the Report Manager web site. Once I set Compatibility Mode, Report Builder 3.0 launched as expected.
Hope this helps save someone else a bunch of time.