Unplug your RK2's RK3's and any other input type devices one at a time until you see your emitters stop blinking or turn off. once you are able to determine what device is locking things up you can then zero in and figure it out.
I agree that you should turn off IR passthrough unless you really need it. It causes trouble quite a bit.
If you can't find the culprit then try shirnking your system down to just one input device and make sure it works perfectly before adding one more at a time and work through it to the end.