Here's your fixed save.
As stated it would have to be Jedi_Found 4. Odd it was 5, even more so if you didn't even FIND Vrook (he will appear in Khoonda after the events you described).
Jedi Killed shouldn't be 3 since you didn't kill Vrook yet, but that's an M4-78EP issue (Vash shouldn't raise it but does), don't think that causes the other issues though.
Also, oddly, Atton is present in your save in the Dantooine area. That, too, should not happen.
Some really weird stuff going on.
So, do you run other mods aside from those mentioned? Other weird occurances? What order of planets?
000017 - Game16.rar