I have not seen that particular issue, but then again, I've never used SBUU to install 2008R2.  I have R2 on all my 2800's and 2850's - all installed directly from the OS DVD (or USB) with no problems.
I'm trying to install Server 2008 R2 on a PowerEdge 2800.  I've downloaded the latest System Build and Update Utility as well as the Windows OS Install Support Pack.  The install begins, I select Server 2008 R2 as the OS and it gets through the first reboot where it requires the OS media.  I insert the Server 2008 R2 and it comes back with the message: You chose to install 32 bit operating system.  However, the media seems to be a 64 bit installation media.  Please insert the correct media or choose another version of the operating system. There is only one option to select Server 2008 R2 and R2 is 64 bit only.  Has anyone else came across this issue?
PowerEdge 2800 and Server 2008 R2