I have yet to upgrade to 10.4.7 myself but hopefully this will help. You list keychains you have at the end of your message, I noticed you didn't list a keychain called login. This is a special keychain that gets unlocked when you log in to your user account (the password for the login keychain is that same as your user account password). It is the login keychain that you should be using if you want to be able to add things to the keychain and never have to worry about them again (ie, automatic logins for adium or websites).

If indeed your login keychain is missing (maybe it got corrupted or deleted somehow) then all I can suggest is that you make a new keychain (look in the file menu, by the way, I assume you are using the application called 'Keychain Access' right?) and call it login (lowercase letters). Now hopefully everything will work like you want (assuming OSX is clever enough to know this is supposed to be the login keychain from its name alone). Also, if this works, you may find that you no longer have to add keys manually, you might be able to use the dialogs that popup when you enter login details at a website for example.

Good Luck!