The trick is to follow the USS Rover from base to base and only kill the spawns at each step along the way. Do not go on ahead and kill all the spawns and then go back to the Rover. Stay with Rover the whole time. Let the enemy ships fire on it and then move in to clean up at each step.
Do it that way and the mission works perfect.
Yep, this is where I went wrong, went ahead on the last tower .. defeated the ships and turned round to find him disappeared .. (sigh) part complete.
Dropped the part mission for this second of the patrol but no luck, it came back with the completed stage and no SS Rover to defend. Hmm maybe a relog.
Well this is silly. Dropped the whole complete sector patrol mission, repicked it up and not only did it remember the 2 system completes I had but also registered the 6 towes I had defended against rofl, so still not complete despite a relog.
Aha, there we go. Jumped to the last system on the list to do and then came back and the SS Rover was back and this time I made sure I was no more away than 6km at all times and waiting for the enemy to attack one of us first.