With RF4CE the STB won't be transmitting (except during the pairing operation) and the remote will only transmit when a key is pressed. So if the alarm is having a problem when it is being set, ie you are leaving the house, there shouldn't be any transmissions from the new kit.
Is your V6 connected to the SuperHub by Ethernet or wireless?
The alarm sensor may be operating at the limit of its range as (according to the website) it relies on mesh connections between multiple sensors to extend the range. Changes in the weather and overall RF environment from other devices, neighbours etc may have pushed it over the edge. If you have a movable sensor (eg PIR movement detector) try positioning it between the problem sensor an the main control unit and see if that helps.
BB
Well that's what I think, but I only work here (at VM)