Bad news, I've checked yesterday and yes, Blender isn't stable with FFMPEG. It's like incompatibilites between API used by Blender and the lib I've got (from Fab1, but it's recent version and Blender uses API of an outdated one ).

As the whole system crashes without the time to print anything in console its difficult to solve just in 1 or 2 days.

Anyway, I keep you aware.