Please make sure that you uploaded the patch, not the full version, if you uploaded full version then ffmpeg binary may be overwritten. I would suggest to check if you are using the correct ffmpeg binary for your OS (by default ffmpeg for Linux is provided) and permissions are correct - you can recheck permissions here:
Admin panel > Tools > Host Tools > Permissions.

It shouldn't be related to the patch, this patch doesn't change anything related to video files uploading.

If you see more still have problems, please describe it in details in the forum:
http://www.boonex.com/forums/