1. Please make sure you use the newest version of Freemake Video Converter. You can get it here.
2. If the previous step didn't help, please follow all the steps from this guide.
3. Make sure that the original video doesn’t have any issues. Watch it in a media player.
4. 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.
5. Please make sure that your graphic card drivers are up-to-date.
6. 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 an audio sync issue.