I can't explain the first bug, except for the fact that the Kray Dragon fight is a seriously scripted event and messing up something in the Dune Sea by using codes might cause the bug.
The second one is somewhat strange. In the main quest line, LS end, the whole Academy IS supposed to turn against you and close it's doors afterwards. But you shouldn't be invincible whilst killing the students. And it should only trigger if you have past all Sith tests (which ends with the Korriban Star Map).
Hope this helps a bit...
