If you are downloading the .torrent file when you are logged in then regardless of where it is seeding from, that file should be adding points to your account. The issue is the logged in part. If you weren't, then the .torrent you downloaded won't have your unique key. Also, you didn't by any chance have your key changed after you downloaded the .torrent files right?
If you are seeding from two locations then you might see some funny business for a bit but it should all update in the end. It just takes a little longer. Also the tracker decides to be lazy on a few days and doesn't update until hours and hours later. Otherwise, I don't really know what to tell you other than to check your keys in the .torrents with the one that shows in your settings panel.
