Right, system files are easy to replace. But many of them, when you register them write their info to the registry. And in the registry you have services, drivers, every core in windows with settings in the registry that point to other parts of the registry.
Windows 7 I think has over 1 million reg keys.
When you do a repair install it is just doing an upgrade to the same version. Well a lot of those reg keys are kept as it is an upgrade. So if the corruption is in those keys the repair install wont work.
Only way to get it to work is a fresh install, which is where the registry is rebuilt from scratch.
The SFC stores info in the reg and inf files I have found SFC is not always correct.
There is a trick I have done that might help you avoid a reinstall.
Go into safe mode, go to the device manager.
Under "View" click on show hidden devices.
In this mode you will see all old hardware ever hooked into the system, they will be dimmed out a little.
Go into every category and start removing all the dimmed out devices. (Right click and uninstall) and remove any that have an exclamation as well.
The drivers and regkeys for them are screwed in the system. I had a user on XP where is cd rom drives wouldn't work and some other things. When I did this trick it took me about 20 min but he had so many dimmed out devices that it took a while.
When I removed them all from safe mode and rebooted Windows detected what it needed and everything stared working. Uninstalling the devices removed the reg keys for them and luckly it cleared the corruption.
It is worth a shot
Shane