I recently ran into 2 scenarios where the unmanaged layer would not get updated. Both have been confirmed as a bug and will be available in future Rollups.
There's one that should be out with Rollup 12. The scenario for this bug is if you make a label change and try to deploy it with the same managed solution (upgrade) then it doesn't work. If you however create a new solution with just that entity that has changed, the change gets pushed out.
One of them is due out in Update Rollup 14 and it has to do with how multiple solutions were layered. It failed to pull the label from the correct solution.
Thanks,
Linna