Lander in flight, game says it is landed and not moving and cannot add any Man. Nodes, etc. - not sure where to start with this one...

[Iam aspaceman]

I landed a ship on Minmus to satisfy a couple of contracts - one was for a tourist to visit the base that was constructed there.  First off, the portions of my base that were inflatable (Wild Blue's Pathfinder mod) were gone.  There had been no update or anything that would have changed the game contents since it had been built (though I did do a couple of the exit / restarts to prevent those wonderful game crashes).  So, ok, strange but not unheard of - something spontaneously exploding due to vibration, uneven setup location, etc.

I connected a crew tube (again Pathfinder) from the lander to the remaining colony elements so that the tourist could "visit" the colony.  She did, contract complete.  I moved 3 Kerbanauts to the base, another contract complete.  All good so far and making money.  Transfer everyone back to the lander, remove the tube, and take off.

Here is where it gets strange:

I get to an Ap of 6km, oriented for creating a stable orbit, go to map to start adding maneuver nodes...and no trajectory line (or whatever the blue line showing Ap / Pe is called), the lander is now classified as a "base" (which I assume is due to connecting it while landed) it is obviously 4-5km above the surface and moving, but when I clicked on it, it says that it is "landed" at 0km.

There is no error or crash logs to link, obviously a modded install, but other that the updates that Roverdude posted for his mods, there haven't been any updates to the game ( am not using any of Roverdude's mods for this base) - and those updates were installed before I had even added the Pathfinder habitats, etc.  I use several mods, but have never had this issue or anything close to it come up, so not even sure what information is useful to help sort it out.  I am at work atm, but if anybody has any ideas as to where to start to "fix" this, when I am home I can post the information.  The lander itself is 100% stock other than adding a KIS inventory container and some food supplies (Roverdude's Life Support).  What I have NOT done yet was to go to an earlier save game and load it...which will be my next step.