Lorenzo,
Glad you're so happy with JFBConnect. Hopefully your current issues are pretty easy to resolve.
For AUP, go to the Social Configuration -> Misc tab in JFBConnect. Make sure the "Alpha User Points Integration" setting is enabled. Yeah, it's hidden. We need to make that more clear.
In the same Social Configuration area, also go to the Notifications tab and make sure you have the proper email and notification settings enabled there.
Finally, for the Comment plugin not posting to walls, I'm not sure if that's related to any of the other issues you mention. That one, we may need to see in person though. Can you give a URL of a page that doesn't post to the wall? If the site is in offline mode or restricted, that would likely be why Facebook doesn't want to post it. You can also run your page through their URL debug tool to see if they note any errors (any of which *may* stop them from publicizing the page):
developers.facebook.com/tools/debug
Hope that all helps, and good luck!
Alex