Hi Everyone,
I posted the problem on the Matrix Games Tech Support Forum and received a very quick response.
The problem is I populated the QE with the F35C variant which the database does not support for the QE class. It lets you add them but won't let them back on board

. Its a pity because I like to do all sort of 'what if scenarios'. So beware if you upgrade any platforms with better spec' aircraft.
Its good to see that Command is still being developed and is so well supported though.
Hope this is of help to others.