evarsanyi,
I've gotten around this in the past with another application (ActiveHomePro CM15a) by using user settable "flags" or X10 "dummy modules". This allows your second program to test the flag or dummy module state prior to executing.
I'm a newbie with the ISY-26 (2 days), but from what I can see neither of these options exist. Possibly a suggestion for future releases?
As upstatemike indicated, I believe you need a separate qualifier for your RF2 trigger.