I've been a way for a few days, while this thread gained some exposure. I'll also ofer my apologies to Marco.
However, the problem is his speakers.
He will not be able to set up his system properly using the auto or manual features of the RX-V2400. Yes, he will be able to effect some control over the sound at higher frequencies up to about 10K-12KHz. But the paramatric equalizer built into the Yamaha (when using the Yamaha mic) will not do what it is suppose to do when there are huge dead zones in the speakers output. Not to mention that there is probably no clearly defined axis after a couple of inches from the cube itself.
The Yamaha system attemps to equalize the response from the speakers. With these dead zones, and with the speakers conected to the "sub" it will not work.
First, connect the speakers to the receiver - not the sub.
Second, connect the "sub" to the B speakers jacks on the receiver.
Third, in the Yamaha set up, choose "NO SUB", and set speakers to Large.
Fourth, Try it again. (Probably still will not work.)
Fifth, Take what you have back and get better speakers.