i think i have a solution
like you Thrawns shuttle kept circling around the base, the ISD Grey Wolf never arrived and the Correlien Corvette never left base.
i did things things in this order:
- browse the Nebulon B Frigate in your targeting computer
- store it at position F5
- press F5 then "A" to select those units that are attacking the NBFRG
- clear the rest of the fighters
- this is only necessary if the NBFRG hull strength is above 50%.
if it is. attack it with your laser cannons so that Thrawn will enter his shuttle
- now attack the base with missiles to lower its shileds to 0% and its hull strength to less then 50% the Corvette will then leave the base and the ISD will arrive and primary mission complete.
- Make sure thrawns shuttle safely reaches the Grey Wolf when it does your primary and secondary goal will be complete