Everybody forgot about first thing in that type of situation: Have you reinstall freelancer and discovery mod ? I was having some time ago similar problem. I update discovery mod manually and after 1-2 min. undocking from base, i get mega low FPS drop.
EDIT: Oh and you say that happen after Update 3... so did to me *sigh*
EDIT2: Try to update with "Update application". Download and then files will install automaticly.