Mike,
I just registered, logged out, and then logged back in and got both the status messages. I can post a picture if you really want to see them.
As for duplicate messages, JFBConnect simply looks at the last feed message posted to your wall and, if it's the same as what's about to be posted, we won't post it. There are different types of messages in Facebook, so it may not be the 'last' post in your wall. It all depends on the different things that are posting to your wall. In general though, things seem to be working well for your site.
The duplicate message functionality there is in order to protect your application from users marking excessive posts to their wall as spam, and is important to do. It was added in the v3.4 release, I believe, which may explain why you're seeing less posts.. but again, it's good that your seeing less. Facebook is on the warpath against 'spammy' apps.
I'd recommend testing with other accounts, more status updates between logging in (some with URLs and images, as those are different status types), and see if you see the message come back again.
Good luck,
Alex