I've experienced the same issue. There are two possible solutions:
1. The fix for the moment is to manually add the missing one to True Key, and the next time you visit the site you will be asked to choose the correct login from a list.
2. The other option is to edit the password form dmv.ca.gov, click in the "Advanced" tab and make sure the option "Use for dmv.ca.gov subdomain only" is enabled. You might be able to do the same for www.ca.gov.
Hopefully one of those options will work for you.