I don't know if this is part of your problem or not, but I do quite a few installs of computer systems, and I do install Acrobat (currently 6.x) as part of the setup. Many times the first time it loads there is a box telling you than an update is available, do you want to download it? For some reason that box seems to stay hidden, behind the main Acrobat window. I also thought the program had stopped loading until I discovered this "feature". So now I minimize the main window after loading, just to ensure it's not lurking on me.

Good luck,
Bruce