I've posted this issue here, I would request folks who are facing a problem with this please VOTE for this issue with the ffmpeg team so they can fix the base code. Therafter I'll be able to integrate it back into MCEBuddy.
https://ffmpeg.org/trac/ffmpeg/ticket/2078
Click on Up Vote on the top of the page under the Roadmap button. More votes = faster fix. Add you comments if you'd like to speed it up even more.