Ok, as is typical of me (as you will soon learn) I went and picked at the game using what you told me. It seems that the W and S keys override the throttle controller, atleast once you get above 50m/s and out of VTOL range.
When in VTOL range, if you have the throttle at anything less than around 2/3, the ship refuses to accelerate past double-digit speeds (40-45 range). But once you're moving faster than 50m/s, the throttle controller is completely overriden by the W key. It didnt matter if I had the throttle pulled fully back, the ship stayed at full speed if I held the W key.
Now, as before, when I keep the throttle full forwards, when I let go of the W key the ship will -very- slowly decelerate from the speed I left it at. And when I pull back on the stick, it's like hitting the brakes.
Is this as it's intended, or am I missing something in my caffine deprived state?