I've used the portable version - add the videos to the main window and choose mp4 from Setup > Video. http://www.videohelp.com/software/MkvToMp4
Was most probably another program as like attar says you have to use the add button,there isn't enqueue multiple titles option (tho the add button allows multiple titles to be added), & there doesn't appear to be a "save queue option either" which is handy to do in case the app crashes.(had to download it as i've never heard of it) May have been handbrake or vidcoder you were thinking of or not