>This has less (or no) collisions http://msdn.microsoft.com/en-us/library/system.security.cryptography.sha256(v=vs.110).aspx

Do you know why this one is a better approach to have a better success at detecting duplicates?

Also, there is a line which puts the pointer at the beginning of the file. Isn't by default an initialization of a stream to have its pointer at the beginning of the file?