Possible fix: Have constructors queued for bases always come after any ships ordered by the player, unless the player moves one of them up on the list.
And yes, Move To Top would be a very handy button in that list if the auto-queuing stays as it is. Maybe a double-click instead of a button?
[Edit] And now that I read the thread a little better, I notice I should have seconded
It would also be great if any ship you queue would be build before any autoqueued constructor automatically so you don't have to press the top button every time you queue a ship.