I've lost five characters now due to the same glitch, and I've narrowed the cause down to this mod.
After upgrading my ship the second time, when I try to beam back to it, I get stuck in a beaming animation and the game continually beams until I force the program to close. The character is then visible on the selection screen, but the game won't actually start if I attempt to play as that character.
Is there maybe something wrong with the third-tier ship that causes this?