I have had QoS turn off today on both our external connections (it was only enable on those 2). Unfortunately I can't narrow it down to anything specific, as I had done both a restart and interface enable/disable (chasing an unrelated problem which turned out to be elsewhere in the network).
I haven't spent a lot of time on this one yet but I do have the same issue.
I was having a WAN connection issue, disabled the PPPoE connection, rebooted, enabled it and noticed QoS was disabled some time in there... I will do further T/S when I have time.