I have the same problem.
When I worked at Zeroshell 1.16beta QoS+ L7 work perfect.
Properly recognize all the packages (SIP, RTP, HTTP).
After installing 2.0RC2 and 2.0RC3 (2.0RC1 caused Kernell error) QoS does not work properly with the L7.
Zeroshell works as the main router.