Originally Posted by Achilles
Sounds like you're missing the 2nd tree. It's been so long that I don't remember the exact option, but I'm pretty sure that it's a continuation of the first. If you have DLGEditor you can open up HK47.dlg and check for yourself, otherwise I'll try to remember to look when I get home.
EDIT: BTW, I've always gotten both bonuses, so I know they're there.
I think I found the second one. It seems to be activated after:
You run into Darth Sion on Korriban. The dialogue tree seems to be how to deal with Jedi/Sith that just won't die.
There are two points in the first bit of dialogue that mention bonuses, one mentioning a reflex type bonus and the other mentioning wisdom and constitution bonuses. Both award 1000exp (I think) since I ended up with 2000exp after I finished speaking with HK-47.
EDIT: To clarify, after I got the 2000exp, the bonus on constitution and wisdom were only +1 each. So I'll have to wait until after the part in the spoilers to see what happens.