It's possible that because the label overlaps contacts, that when the circuit is flattened, the label gets disassociated from the metal. If that's the case, then it should be relatively easy to code up a fix for it. And if that's the case, then you can apply a workaround solution by making the labels smaller so that they do not overlap contacts, or else just set the label property to "sticky" using the "setlabel" command.