When my ship is within the atmosphere, on an exoatmospheric trajectory, the landing prediction deactivates, and instead gives me a "predicted orbit after aerobreaking" with a negative periapsis.
I am not sure whether this is a missing feature or a bug, but I looked at the changelog: http://wiki.mechjeb.com/index.php?title=Version_History#Version_1.8
"Will predict landing site even for trajectories that go exoatmospheric to enable targeted suborbital hops"

probably would need to get addressed by #1052