It sounds like the Repeater Target might be changed to something you aren't expecting, in that window. The only way this SHOULD happen is through a Repeater Target Action. There are other ways it changes, but they SHOULD be temporary -- Send Next Click, Repeater Regions, Video FX with repeater built in, etc.

You can force the Repeater Target back to normal if you like. In your Activate Repeat mapped key under Control, in Step 1 where it turns ON repeater, add a Repeater Target Action. Set the Target box to Window:Current, New Repeater Target to Window:All w/o Current, and don't check the "block" box.

Any Export to Inner Space will also reset it to its original state.