It's puzzeling that one amp came on and the other didn't. Obviously the 990 is sending a signal, so the problem must be downstream. The second IR port should work, but make sure you have your configuration set to send a signal for the input your selecting. I don't believe an IR reciever is even necessary. I haven't had need of the second signal port, but as I understand it, it sends a signal whenever you select one of the inputs configured for that purpose.
Good Luck!
Let us know how you solved the problem.