for certain ProRes files.[prores @ 0x7f353cfc9a00] alpha channel not implemented. Update your Libav version to the newest one from Git. If the problem still occurs, it means that your file has a feature which has not been implemented.
I've updated avconv/avlib, which created a bunch of new errors (i don't remember the exact error, but it was something to do with 64bit and libavformat.so 'not valid symbol') so i've uninstalled avconv which has got me back to where I was.
Any suggestions?