usasma asks some very good questions, please address those first.
You say that all drives are ok when you check them manually ... but you also say that you cannot boot into Windows, so you must be using a live disc of some kind. Please identify what you're using to boot and run the utilities (chkdsk, regedit, chkNTFS, etc).
I also wonder if the System Reserve partition might be the culprit - it normally doesn't have a drive letter. There's also the EFI partition - but only if you have an EFI capable system.
When you get the chance, could you create a Minitool Partiton Wizard boot CD
Minitool Partition Wizard: downloads
scroll down to the bottom of the page and pick:
MiniTool Partition Wizard Bootable CD allows user to boot computer directly into MiniTool Partition Wizard to manage partitions without any limitations.
Then boot from the PW disc and post a screen shot (a camera or phone will have to do). You can also check the drives for errors with PW, but you've already indicated that they are clean - at least the ones you tested.
I'll be off until next year.
Have a great last night of 2014!