I might guess that the Repeater Target is munged in that instance. The "Activate Repeat" mapped key for some time now has a Repeater Target Action at the top in order to reset the Repeater Target back to "Window: All w/o Current".

If you're using an older configuration (e.g. originally made with a pretty early build of 40, or anything prior to 40), then you might not have this and so it would keep whatever the current Repeater Target is. If that's the case, it's entirely possible that some sequence of actions involving Video FX with broadcasting or Repeater Regions or something might be leaving the wrong Repeater Target in this window.

This is the only thing that comes to mind from your description.

Actually now that I test what I just said, it appears that the Activate Repeat that's in the WoW config does NOT reset the Repeater Target, just the non-WoW version. I'll have to update the generated WoW config with this change, but anyone with this issue currently can do the following....

So I guess here's my suggestion. (Add the described Repeater Target Action)
1. In the top left pane under Key Maps select Always On
2. In the bottom left pane under Mapped Keys, expand "Activate Repeat" so under it you see Steps, 1 and 2
3. Click on the 1 under Steps
4. In the bottom right pane, right click Actions and, under "Repeater Actions", select "New Repeater Target Action"
5. To the right, you will need to configure this new Action's properties:
5a. Set "Target" to "Window:Current" (or "Window: All w/ Current"). This affects which window(s) will change its Repeater Target.
5b. Set "New Repeater Target" to "Window: All w/o Current" and leave "Block buttons" unchecked. This is the default Repeater Target when you start up ISBoxer
6. Now move the new Action to the top of the Step, before Repeater gets turned on. You can either right click the Action and select "Move Up", or select the Action and press Alt+Up (or Alt+Down) to move it
7. Export to Inner Space