I wonder if you can run
error checking and sfc on the external drive?
You can run error checking on an external disk with CHKDSK, but SFC (the system file checker) is purely for the OS files. The system holds duplicates of important system files in the so called "mirror" and it compares those files in the system with the mirror. If the system files are corrupted, it replaces them.
But it does not have a copy of all files in the mirror. That is why it sometimes cannot repair some files. Those you can repair with a Startup/Repair with the System Recovery Options menu, which is on the Windows 7 installation disc. The disc, of course, has a copy of all files in the system.