This is a long shot, but I just installed 9.0 on Vista Ultimate 64 Bit SP1 and have a similar symptom. In my case, I understand a small piece of the problem, to wit:
My users homed on C: can run the Reader with no issues.
My users homed on D: cannot run the Reader (Stopped Working).
Does this sound familiar to anyone? If so, is there a known fix other than moving the users to C:?