1) Don’t worry for the warning. I will try to remove it in the next release.
2) I think the QoS classifier is being confused because you created double rules (downstream+upstream) and class for any protocol. You should create only one class for type of traffic and assign the bandwidth parameters in the Interface Manager. The local QoS parameters of the interface ETH00 is for shaping the downstream and the ones of the interface ppp0 (WAN with PPPoE) if for shaping the upstream.