When EFS encrypts a file, it copies its contents into a temporary hidden file. It then encrypts by blocks and writes the encrypted data into the original file. After the process is done, the temporary file is deleted. To guarantee erasure of the file you need to wipe the freespace and the file...
Probably your drive has a fault. Running eraser could have hit the bad sectors. Just by creating a new document would trigger the same effect. If you can attach the disk to another PC, you might be able to read the contents otherwise its time to use your backups.
I assume you have done the windows update? This sounds like an issue with your .NET install.
Have a look at this link http://blogs.k10world.com/technology/delete-net-cache-versions-server/
Might help but make sure you understand what you are doing.
Are you able to 'whitelist' an application in your malware scanner?
There is no reason that eraser might not erase a particular file type unless its being affected by another application
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