It almost sounds as if you have the ir ports addressed wrong and the only reason its working is because of the ir from the remote itself.

i would do the following.

1) verify all codes work with ir from remote to component first IMPORTANT

2) then set mrf to "0" to check for rf interference

3) then pick a channel, say 1

4) set software to use channel 1, turn off ir output

5) turn up gain on antenna

6) get someone to help and walk around house hitting any button and look for the indicator light to flash. Position antenna so it works all the time. if you get interference with antenna gain all the way up, turn it down until it goes away and/or relocated antenna.

7) Once you have the mrf300 getting reliable signal from the remote THEN connect the flashers to your components and route the ir in the software to the ports that the flashers are connected to.

8) Verify flashers are flasing on the proper components. (ie Volume changes are actually flashing reciever, play on DVD actually flashing DVD)

9) At this point you should be in good shape.

It's important to go 1 step at a time when troubleshooting these things. Solve 1 variable at a time to keep from going nuts.

Let us know how you make out