I've never noticed what you experienced, but I always use the keys.
Survey = S
Explore = X
I hope this lets you get your ships doing what you want.
Thanks but I looked it up, S=Sentry, W=Survey.
I did notice whatever command is already active will disappear from the command menu.
However, your survey ship should always have either explore or survey available depending on which command is currently in use.
Anyway, i think ordering it to move at least one square manually cancels any current orders, so try that?
the only other thing that can happen is if you upgraded your survey ship and forgot to include a survey module? For that you also need interstellar travel technology at the very least, plus medium hulls of course!
I think you misunderstood me, or I wasn't very clear. I have no problem ordering them around. I wanted my survey ship to auto survey at this point and because I forgot the keyboard command I just clicked on the Command Menu in the lower left corner to select the appropriate command. I can see them all there, but the Survey and Explore commands cannot be selected or highlighted.