We finished this conversation in the chat room but for anyone else:

Repeater Regions are currently only loadable as entire sets. The set of Repeater Regions that you load contains every single Repeater Region that is active when you click Save As, for your whole Character Set. So if you have 1 region in one window and 2 regions in another window, and you click Save As and name it, say, "BG", then the set contains 1 region in one window and 2 regions in another window. That's exactly what will come back up when you load that set, either from the ISBoxer Control Panel, or a Repeater Regions Action. "Auto" is automatically loaded when you launch your set, or Export to Inner Space.

So in TheLostBoxer's case he was asking me about having a region for 5-man and a different region for BG's (10, 25, 40, whatever). That's relatively normal, I always had the same thing. Save the 5-man as the Auto set. Then to make the BG set just clear out the existing Region or move it around and click Save As to save as BG. Then either set can be loaded manually through the ISBoxer Control Panel with the drop-down box + Load button, or with a Repeater Regions Action (which does precisely the same thing as selecting a set in the drop-down box and clicking Load). When you load a set, all regions are cleared out, and replaced with the new set.