There is your problem. When you renamed you're file you called it "Input.pdf.pdf"
type this command instead
Code:
sopdf.exe -i input.pdf.pdf -o output.pdf
or rename the input file
Code:
Prompt> move input.pdf.pdf input.pdf
Prompt>sopdf.exe -i input.pdf -o output.pdf
What happens is Windows Explorer has this "feature" that hides the extension. When you rename a file and think you added an extension it does not your only adding the filename.
The command line however does not do this and requires the exact file name.
I hate that feature and disable it immediately.