Did anyone solve this problem?
I just upgraded from 5.5 to 5.7 and this happened to me too. Everyting works fine and whitout warning mysql just hangs and starts to fill log. Only way to fix this is kill mysqld and restart it.
mysql Ver 14.14 Distrib 5.7.17-13, for debian-linux-gnu (x86_64) using 6.2