While what Vishwa said is most likely correct, i prefer to think of it as Jim being woke up because he is:
but instead of fixing the problem, he spends an entire year playing video games and growing a beard until he finally sparks interest with a lady and investing all his skill set in waking her up.
Later another character wakes up - this time most likely due to malfunction, but maybe also as a further escalation step because Jim obviously isn't taking any hints. At this point he gets some clear goals and quickly achieves the goal by throwing a hail mary in space.
Unfortunately, the ship would have had multiple means (Arthur, Displays, Announcements, etc.) to give him clear instructions earlier on. So chances are that he indeed woke up by a malfunction as well.