thats the funny thing about coding, it can work fine in one mission, and in the next one it doesnt work at all...
im wondering if the collision on the Theseus pods, or something related is not triggered when the order to return is given? is it turned off at all? or is it related to the ability to combat dock? what things are triggered when the order to return is given? im assuming the pod deck changes state from being a solid object that you can crash into, into a modified solid object with docking characteristics? maybe it gets stuck between the two states? that would explain the lack of collision and the inability to dock...but it is only a state change on the pods, the main hull of Theseus remains the same throughout the mission...
maybe changing the mission to allow for combat landing at any point of the mission? of course this would end up in a failed objective state, or less than desirable outcome, (which could mess the story line tree up a bit for the player if they choose to land prematurely... i guess) but might be a solution...
im not sure what killed me, maybe the Indart blew up, or a raider shot me through the hull enough times to whittle me down below a safe percentage so when i was finally naked (when Theseus jumped) it was an easy kill? not sure, i was too focused on trying to land...