Sean,
Generally, the Like count changes when the URL structure for a page changes. It shouldn't really change on your home page as that shouldn't change much. However, with that said, I did a little bit of playing around. Using the
Facebook Like configuration tool
, I plugged in a lot of common values for what might be your home page. With and without www, with and without http://, using https, etc. I finally came upon one URL that showed 65 Likes:
www.carjersey.net/index.php
I'm not sure how you were implementing the Like button before, it seems you wer including the index.php in the path to the page. I'm assuming you were doing something else and moved to using JFBConnect. Either way, to show that Like count, you'd need to update the JFBCLike button to include the index.php as well. That shouldn't be a problem, but it's up to you as that will show the index.php in any links that show up in a user's feed after they've Like'd your page.
Hope that helps explain,
Alex