Yeah, overlapping rooms don't always behave... sometimes they grab whatever's in their bounds (so, whichever one you grab, picks up the overlapping stuff), sometimes not... and polygons don't reproduce at all (unless that's been changed recently, I forget).
It looks like you're using pairs of rooms here, maybe you should add a hierarchical level, one up from these, that includes both? Then there's no overlap, it's all in one room. (Just disable the unused rooms in Project Settings/Classes.)
Tim