vendors put on hidden partitions so they can put a hidden copy of windows on it.
there are also reserved partitions, different sizes are required for different versions of windows.
generally the hidden partitions will not have a drive letter assigend to them but when you plug in another drive windows detects the drive and will assign new drive letters to all the partitions that are not reserve partitions.
kind of a bummer, it can result in the OEM install partition becoming drive c: your USB thumb partition becoming drive d: and your actual windows install becoming drive E:
but your boot loader does not get changed and it tells the boot loader to go to drive c: to run winodws.
it is why you would have to run bootrec.exe command with...