Hi,
Are you talking about specifying passwords in the Advanced Auto-Populate tab? If so, passwords stored there are encrypted in the RDF file... take a look!
Yes, they are not stored in plain text format. But PasswordMaker still populates those fields without entering the master password if the field value is not based on the master password.
For instance I have a site where both the login and the id can not be changed by myself. I have to use some default login and password combination.
I set up an advanced auto-populate account for this site for both the login and password field to be filled automatically by PasswordMaker. However, the password data is not protected by the master password. So encrypting the entire rdf file would be a nice thing.