[sgqwonkian]

Is the game paused? I've found that the TIME command sometimes pauses the game. It has something to do with where in the quest you put the TIME command, and whether you have "endquest" before, in, or after your GOTO or YSNO PAGE.

I know you mention nothing about the TIME command in your post, but the symptoms are the same - it's like everything freezes up and the engage buttons stop working. The first couple times it happened, I actually rebooted 'cause I thought it was a hang/crash.
Instead, it turns out to have just put itself on pause. As soon as I hit the spacebar, a bunch of time rolled forward and I could engage again. I've considered doing this intentionally on a quest: "You encounter a space-time distortion that traps your ship between heartbeats." But it seems awfully cruel to be that annoying on purpose.