In Science Mode:
Having done the appropriate research to enable additional levels of MechJeb features (ie: Advanced Flight Control research to enable Maneuver & Translation AND Unmanned Tech research to enable Ascent, Landing and Spaceplane)...
If flying a new ship the features are available and are also available when switching to another ship.
However, if opening a save game and selecting a ship to fly from the Tracking station (which is fully upgraded by default in Science Mode) some features are not available and a msg appears in the MechJeb menu that:
"Some modules are disabled until you unlock the proper node in the R&D tree or upgrade the tracking station"
... despite these features being used on the same ship prior to saving and quitting the game.
This appears to be an issue on manned and unmanned ships and also ships that both do and do not have an AR202 (but do have some form of Mechjeb enabled command and control part).

Occasionally, subsequently switching between ships, repeatedly if necessary, will restore some additional features in MechJeb

.