The problem most likely is not CEC related.
The projector, when it is connected to a repeater (the AVR) or a source device (Blu-ray player) supplies an EDID (a statment and list of the capablities of the projector). It is here that the projector lets the other products upstream know that is HDMI 1.4a 3D capable. The when there is a repeater device (AVR) it reads the projector's EDID, compares it the AVR's capablities and then passes a new EDID to the source device that is a combination of video capablites shared by the AVR and projector and audio capablites of the AVR - it is not just a simple pass-thru.
It sounds like the projector's EDID is corrupted when it goes to the AVR and the AVR is not reading the projector's 3D confirmation. Since the AVR cannot read the 3D confirmation, the AVR cannot pass that to the Blu-ray player. When the Blu-ray player does send a 3D signal, it includes in something called the INFO FRAME the type of 3D signal that is being sent. Neither teh EDID or the INFO FRAME are directly tied to CEC.
There might be settings in the AVR that are interfering, such as scaling the 3D signal from 1080p/24 (1080p 3D Frame Packing from the Blu-ray) to 1080p/60 or something like that.