They should overlap. Trying to do two different designs in one PCB or why do you want the copper to flood on a second board in the same design?

@cjohnson It's one product but effectively two designs.  They are soldered as one with wire links between them, then you snap it and mount at 90 degrees.  Very common approach in the audio industry.

@MikeDB Gotcha. I've had issues being able to get planes to do anything at all, once i've hand drawn the outlines of the next board/panel. One way to get around it (albeit a not so great one) is to select the copper area and select keep solid. It will flood across board lines then, but then you get the pesky isolated copper areas.

@cjohnson I assume you're saying they haven't fixed the bug.  That's a pain.  Have to have a think around this.

@MikeDB I would create a topic for an actual bug report, it's an issue I think.