Even if you are logged in as Administrator, the system does not perform some task as administrator for security reasons.
You must right click on the Command prompt and select Run as administrator.
Command prompt can be found in All Programs/Accessories when you select the Start Orb
The only thing I can offer for this is that if you connect a USB 3.0 device to a USB 2.0 port, you should get a message that this device could perform faster if connected to a USB 3.0 port and no message appears if both are USB 3.0.
You could also run a benchmark test of the drive. This tool...
There must be at least one primary partition for Windows to boot. It would contain the boot records.
You could use a third party partition tool to change the extended partiton to primary and the use the Windows DVD to do a start up repair.