Nope, that's not it.
One point of interest is that if I add an SOIC8 (which is what this is), then give it a random ref des, said ref des mirrors when I swap layers.
However, if delete IC3 (the rogue component), add another SOIC8 , then call this new one IC3, it asks if I want to "Bond to unplaced component IC3". If I do that, it adds the SOIC8 to the ratsnest, but "unmirrors" the ref des. This makes me think it might be something carried through from the schematic. Quite what though I have no idea.
Edit: If I add a new symbol of the same type in the schematic, name it IC6 and import it, then all is well. If I rename it to IC3 after deleting the old IC3...same problem.
![Shocked :o](https://www.eevblog.com/forum/Smileys/default/shocked.gif)
Edit 2: If I add a capacitor which is an example of it being on the top side but having bottom side ink, then adding a new part does not help.