anonymous created the issue
Passwords already registered in a keychain different from ~/Library/Keychains/login.keychain will be read and copied to ~/Library/Keychains/login.keychain (which defeats the whole point of storing them in a different keychain)
The code to read passwords in keychains different from ~/Library/Keychains/login.keychain was included 1ec8991 in 3.1, in order to fix issue #2001
I only checked this using FTP.