If you have other operating systems on the same disk and use another boot loader (GRUB, Darwin Loader, etc.), Vista sometimes refuses to boot and is also unable to fix the problem itself. It will still find the Windows partition (bootrec /scanos) and the partition will be perfectly fine (chkdsk /f /r C:).

To fix, run diskpart.exe:

select disk 0
select partition <other OS partition>
inactive
select partition <Windows partition>
active
exit