Hi Sarah, sorry you've not had a reply.
I want to apologise if any of this patronises you, I'd like to see if we can get to the bottom of this.
This is a complex question and could be any number of issues.
At what times does your helm control "lock"?
Helm is controlled via the arrow keys, sliding the maneuver bar, or clicking on the helm screen itself.
If you're trying one (say: clicking?) and leaning on the other (say: the arrow keys) they'll confict. (maybe)
If your engineer pulls power from maneuver, warp or impulse you will find it "locked" or ineffectual. A routine apology from me is: "sorry, I was trying to setup my presets, that's why there's no power to the engines".
How are you running Artemis? Do you have the standard: one PC server, one PC each for stations, or are you running multiple instances of Artemis on one machine? I've found it doesn't like running multiple instances sometimes and clicks can stop registering, for me it was weapons.
What about the environment? What I thought was a glitch, turned out to be that we were stuck in a nebula that was destroying our maneuvering as quickly as we fixed it.
Have you been shot? Sounds stupid, but I've seen crews go into battle without shields, their entire ship goes bright pink in damage and then when the Captain yells to get out of there... nothing happens.
"We should give him the send-off he deserves. He died saving us all. Prepare a Rocket-Shed for immediate launch."