Make sure you've set the base_url[index] and base_url[(journal path name here)] settings in config.inc.php as well; those should cause emails to use the right URL.
If the problem is in the email signature, you can fine-tune it manually on Journal Setup page 1. There are several other settings that contain URLs that are generated when the journal is created, such as on Journal Setup page 5, and you'll need to correct those manually as well if the URL has changed since the journal was created.
Open Journal Systems Team
Don't miss the First International PKP Scholarly Publishing Conference
July 11 - 13, 2007, Vancouver, BC, Canada