Make sure you use the latest version of Freemake Video Converter. Update here http://www.freemake.com/downloads/. Could you please send us your source file, the file you're attempting to convert? Please use http://www.filefactory.com/
Report me the title of the file, and send its link to us (create a ticket).
What preset for output file did you use? Do you've any custom presets for the output file? Please make a screenshot of it and send to us. Could you please repeat the process and send us all the files from Freemake folder?
You can find them in:
Windows Vista, 7, 8: C:\ProgramData\Freemake\FreemakeVideoConverter\
The files are hidden, so please let them be shown.
In your Windows Explorer go to Tools->Folder Options->View (tab)->Hidden files and folders->show hidden files and folders. Press the Apply and then OK button.