Thank you for the reply JensS. Weird how one card will work and then others won't. I don't know enough to have a clue why, but thank you for posting what did work for you.
@JensS, did you ever get your LSI 9690SA-4I to work with the HP SAS expander? I am having the same trouble as you did in your post (1639 & 1644). I am having the exact same issue as you did about the controller not able to initialize.
Thank you for your reply.