Have a look at this map (http://knucklecracker.com/creeperworld2/viewmaps.php?&mapid=1833). Pause at the start. Select 2 speed upgrades from Technology panel. Give the LS instructions to fly to the upper-left area of the map (to the left of the emitter. Note how it selects a path where the side of the LS will be in the creeper clinging to the side of the trench.
Not expecting a fix, just saying....
Edit: Fixed link.
The link seems to be broken.
If I remember right (or deduce what I probably did), the ship checks the center subcell of each cell to determine if creeper is present when pathfinding. This is an optimization that cuts down on 8/9ths of the work it takes to determine if the ship is over creeper. Or I could remember wrong, and it checks more cells just not the left and right subcell edges. Of course in this case it's better to plot a manual course for the ship to avoid the line of creeper on the left.
i remember thinking to myself no stupid ship you are killing yourself, but a manual course doesn't have any problems.