Are you sure you're unable to move them or are most of them just out of move points? This issue usually arises when for some reason a ship can't be automoved, and cycling through them and making sure they've all exhausted their move points will allow you to continue.

The best way to accomplish this is to click the next button, then hit the space bar. Repeat as necessary. It will waste the movement points of whatever ship is stuck, but it sure beats not being able to finish your game.