This article is probably a few years late, but maybe you're like me and are still primarily using some version of Windows Server 2003 and haven't jumped to Server 2008 yet. I had one server running Server 2003 x64 with service pack 2 installed and decided I wanted to upgrade it to R2. I popped in CD2 of the R2 media and tried installing, but to my surprise it got an error saying "Setup cannot continue because this product disc is incompatible with the service pack installed on this computer. To complete the installation of Windows Server 2003 R2, you will need to insert the latest version of Windows Server 2003 R2 Disc 2.". At first I thought I'd be able to slipstream SP2 onto the second disk, but since the Windows install files are all on CD1 you can't do that. A quick Google search fixed my problem though, so thanks to stealthpuppy.com. Here's what to do in order to successfully install R2 on a Server 2003 x64 server running SP2.
1. Insert the R2 CD2 disk
2. Create a folder somewhere on your server and copy all the files from R2 CD2 to that folder
3. Go to your folder, then into CMPNENTS, then R2
4. Find the file named R2INTL.INF, right-click and choose Open With, then pick Notepad
5. The file should be open in Notepad at this point. Find the line that says "R2SPLevel = 1", and change that to "R2SPLevel = 2"
6. Save and close the file
7. Run R2AUTO.exe from the root of the folder you created in step #2
You should now be able to successfully install R2 on your SP2 installation. You could also burn those files to a CD or an .iso image file for future use.
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