I have the exact same issue, I just installed the game and I'm running the following 
  
New game 
TSLRCM 
Fixed Lightsaber Colors 
  
The first time I started a new game T3-M4 was dead when I got out from the Harbinger, the second time the HK-47 droid is not where he should be during or after the cutscene. 
  
This second bug prevents me from progressing at all and the first one prevented me from getting a companion. 
  
After the first bug I completely removed KOTOR 2 and reinstalled it.