Had a ship that was finishing up it's given orders in another system (move to home system JG, transit, move to home world, refuel) when I added on to the orders to grab a cargo, move to another system's JG, transit, move to that world, drop the cargo. I clicked the checkbox that causes the orders to repeatedly cycle.
Later I noticed in the F12 orders window that the ship was headed for the JG, but on F3 map of the second system was headed on a different vector. I figured out that was using the vector of the JG for the first system, the system it was in when I composed the orders. It did successfully transit back to home system.
Looks like there's a bug somewhere. I couldn't tell if the F12 window was wrong in the time it took to get to the JG, as compared to the F3's view of it's location.