The RF signal just sends the data from the remote to the command center, which then converts it back into an IR signal, which gets emitted from the center and also sent through the IR blaster.

As you're not using the command center for this purpose, all of the IR signal is coming from that one little IR-LED at the end of the IR blaster cable. Seeing as how you have it positioned at the top of the stack, I'm surprised that the unit at the bottom of the stack can see the signal at all.

Another thing you could try is picking up a dual head IR blaster!

Rob