OK, two things come to mind. Firstly, I suppose your game is patched to v1.4? If not I suggest you do this.
Secondly, have your crew been at battle stations for a long time? If so, then they are probably fatigued, and are unable to respond (think of it as the crew falling asleep on their feet).
All you need to do then is to stand down from battle stations, and when the crew recovers sufficiently you can move.
Also, there's no need to restart a career when you apply a patch or mod. Just make sure you're back in port. And even then, mods which change just graphics can be applied mid-patrol, although as a rule I make sure I finish up a patrol before I tinker with mods.
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