Now this has got to be something really simple that I am missing but how do I save a converted file in Handbrake? When I click on Browse in the destination box and then go to the folder I want the video to be put I get zilch unless i click on a video already there which means a box pops up asking if I want to replace the file, which of course I do not. Edit. Doh as soon as I posted I realised I needed to name the file.
While I know you've sorted your issue, I thought I'd add that if you wish you can set Handbrake to automatically output the file into a specific folder by default and name them too. Mine is set to save to the same location as the file I'm using with the same name but adds a -1 at the end, so Video.mp4 becomes Video-1.mp4. If you're interested in this, it's under Tools -> Options -> Output Files, tick the "Automatically name output files" option. My settings are Default Path: {source_path} Format : {source}-1