I have tested the application and was able to convert an AVI file to MP4 without errors which means there is something wrong on your computer or with the application itself. I recommend that you perform a reinstallation, then try converting again.
Additionally, it's possible that the settings for the MP4 profile are wrongly configured or used. Try switching to another format, then switch back to MP4 and do the conversion.
I converted multiple files and the process was OK without errors.
Official website: http://www.xilisoft.com/video-converter.html#
Note: Always use the latest version of the software.