1) replace the ir emitter with a 3.5 mm mono cable and plug it into the ir input on the back of the receiver. It's a much more reliable way to control the receiver.

2) check for rf interference. Make sure the rf light is not lit up on the antenna of the base station. It should only blink when you hit commands on the remote. If it is lit up try moving it or changing rf channels on the mrf350 in the software. Make sure it is not set to channel 0.

3) pull the battery on the back of the remote and reboot the remote.

4) open up the software and make sure the ir ports are assigned for each device and not set to all. Then reload the file.

5) reboot the Onkyo by pulling the plug.

6) re-adjust the ir trim settings as needed.