1. Please make sure you use the newest version of Freemake Video Converter http://www.freemake.com/downloads/.
2. Make sure that the original video doesn’t have any issues. Watch it in a media player.
3. If the original video is OK, then try to turn off acceleration. Start Freemake Video Converter. Go to File->Options->Acceleration in the program and uncheck all accelerations, then retry to convert the file again, it may help.
4. Please make sure that your graphic card drivers are up-to-date.
5. If you have a .ts file, please don’t edit TS video; it may help to avoid such problem.
Check this guide if you have audio sync issue.