I uploaded the "uploads" folder to my wordpress install manually from a backup with the exact domain. All of the media properties for height and with are the same and they are all visible on the site. The only problem is that I can't see them in the media tab. Any fix for this?
First, its not a bug. Its by design. Second, you can try this plugin - http://wordpress.org/extend/plugins/add-from-server/
Unless I am mistaken, when you upload a file in Wordpress, it actually places the file in the uploads folder, but also adds a post entry to the database behind the scenes somewhere. If you are missing that MySQL data for Wordpress to know what to show in the Media Gallery, then they won't show up in that view (even though the files are technically there behind the scenes).
Also, you may want to double check your path in Wordpress for the folder just in case. You can find this at Settings-->Misc