If you allow the Windows 7/2008/R2  setup CD to create your primary partition, it will actually create two partitions, a hidden 100mb system reserved partition used for bootmgr and bitlocker, and the remaining space in a second partition.

I wanted my windows server with single clean partition to make easy backup.

STEP1) Open a command prompt with administrator privileges (right click => run as administrator)

Type:    bcdboot c:\windows /s c:

 You will get a message similar to: Boot files successfully created.

STEP2) Open the Disk Management GUI (you could use diskpart), locate the  C:\ partition right-click and select “Mark Partition as Active”, select yes to the “do you want to continue message”.

STEP3) Reboot to confirm that everything is ok.

STEP4) In Disk Management you can now delete the 100Mb System Reserved partition by right clicking on it and selecting “Delete volume”