If the System Active flags were originally on System Reserved partition as one would assume, then in order to move the boot files to C it requires not only moving the Active flag, but also the boot files while making it bootable. This is done best by running Startup Repair - Run up to 3 Separate Times
which writes the boot files to the partition while making the necessary adjustments, testing all parameters to apply multiple fixes and commands.
This would not happen merely by moving the Active flag unless the System boot files had already been moved to C in some previous operation, or were moved at different times with a combination of moving the Active flag and running one or more Repairs. PW also has Rebuild MBR on its Disk tab which sometimes works but doesn't do the job completely as the Repairs do.
To know this is done completely as only the automated Startup Repairs can do, reboot and tap the F8 key to see if the Repair My Computer option is on the Advanced Boot Options menu. If not run the Repairs until it is.
These are not mysteries to us as we deal with them by the thousands here since before Win7 was released.