Thanks for the feedback!thanks for the update eventure... the mega ship missions kinda worked when I first accepted them, but then when I got to my fleet carrier they had disappeared from the list? and arent showing on the TCE mission panel any more.
My thoughts are that the code that is counting the number of active missions isnt counting the infiltrate mega ship missions and so the panel isnt showing them (as they are the last 3 missions I accepted).
I finaly found the last bit, which prevented the mission from being displayed correctly. It was accidentally classified as complete after accepting the mission.
The update above (1.9.0.2) fixes the issue.