Thanks for the repro steps, it really helped (I am more of a VFB->IR guy, that's why I didn't reproduce it.)
Adding to internal tracker (Internal ID=683950640).
In the meantime, what worked for me was re-running Interactive in the VFB after (long-press Render and select IR), it moved the checkboxes to their correct position and kept them there even after closing VFB and running it through the Corona Menu (not VFB).
Thanks,
Jan