Nothing like a good squinting in the morning.
Sadly your in-game widget positioning is not reflected in the ISBoxer Toolkit profile.
So first of all, you can go to each window and move the region manually if for some reason the Sync button doesn't work right. That is certainly interesting, I don't see how this region could Sync to the right like that; I'll have to look into it.
Secondly, when you click Save As in the Repeater Regions tab, it will save all regions in their current position in each window. If you save as "Auto", it will restore your Repeater Regions to exactly as they were in each window when you clicked Save As. If you Save As anything else, you will need to manually Load that Set.
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