First of all, I'm sorry to hear you are having problems.
The leader dying making the flag disappear is by design. If the leader dies, you lose control of the unit, until you give it a new commander. You can do that by openning the Hierarchy Tree window and dragging a new leader (a platoon leader or company commander) into the leaderless formation.
You are probably getting the "Mission complete" message because the unit is aborting the order due to losses. If a unit drops below a certain strength, it will abort execution of its given mission. You can adjust this level by changing it in the property sheets that appear when you assign the mission.
As for the path finding problem, I would suspect that it hit another obstacle and attempted to "re-bypass". But to be sure, I would have to see a saved game. If you send a save game to:
[email protected]
I will check it out. Again, sorry for the problems.