Do you have your OS set to suppress filename extensions? I know that when I use VLC to transcode the output file gets renamed to the same name as the input file, but with a .mpg extension attached to the end of it. Maybe your input filename has a .mp4 extension that you usually don't see. For example: IF = sample.mp4, OF = sample.mp4.mpg. If you tell the OS not to display extensions for known filetypes then you would see the following: IF = sample, OF = sample.mp4. That's my best guess at the moment.
If you play the file using a media player what format does it report?