One of my team mates failed to install the DPM (Microsft Data Protection Manager) agent on a Windows 2008 R2 server. He digged into this issue for a while and finally fix it.
The issue was caused by that the OS boot attribute is on a FAT partition named OS, which I think is the default setting for Windows 7 and 2008. The workaround he used is to move the boot attribute off the OS partion and place it on the C drive. Here is the command:
C:\Windows\system32>bcdboot c:\windows /s c: