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.