The Likes for your website are different than for your Adverts and Pages in Facebook. However, the Fan module, I think, should reflect how many fans your Page has. That's as long as you've set the same Facebook Page ID to the correct Fan Page id.
If you are still getting different results for the Fan numbers, feel free to post a link to your Facebook Fan Page and your website, and we'll see if we can see something that might be off.
Synchronization the LIKE AND FRIEND with Adverts and Pages
