Did you ever get to the bottom of this issue? We have exactly the same symptoms. Our boundaries and boundary groups are correct - nothing overlapping.
A slight difference we are seeing is that we get this when using client push as well. The CM12 client clientlocation and locationservices look OK for a while and then they "rotate" back to the CM07 MP again. The assigned site always stays as specified to the CM12 site, but stil they get assined back to the CM07 MP.