To launch an application inside RR you should use the LOAD command and make a screen for it. The RUN command is meant to launch programs that run simple tasks and finish in a brief amount of time, meaning you shouldn't run full blwon apps with it (that's why it sort of works). There's a whole FAQ on launching an application embedded.
Regarding IBUS flashes, you should be able to reprogram the commands from IBUS, add: SET|| in front of your commands.. this will prevent RR from flashing. For instance, if your command in IBUS is "NEXT" then change it to "SET||NEXT" this will prevent it from flashing when IBUS sends the command.