Sometimes when sitting in the captain's chair, the game gets stuck. That is, the characters keep moving and doing their stuff, but your own character gets stuck without continuing to the captain's view. Your only alternative then is to load a previous save.
I seem to recall it happened in the original game as well.
This sounds like another manifestion of bug #3037665: "SQ5: Frozen Script":
http://sourceforge.net/tracker/index.php?func=detail&aid=3037665&group_id=37116&atid=418820
Since they are unstable/timing dependent, they are very hard to investigate, so please be patient while the SCI engine team investigates this.
This is a game script timing bug, and it's very hard to fix. It's the same as the one tdhs linked, and it's already in our SCI bugs page:
http://wiki.scummvm.org/index.php/SCI/Bugs#Space_Quest_5
Closing as "later"