After upgrading my iMac to El Capitan, I started getting annoying popup windows from various apps asking me to enter my keychain password because they wanted to use my "login" keychain.
A call to Applecare provided the solution. Here is what they had me do.
In Keychain Access, which is in Applications/Utilities, go into Preferences.
In the General tab of preferences, press Reset My Default Keychain. After it is reset, go into the Edit menu and select Change Password. The AppleCare technician said to make sure the password matches my login password, which it already did, so I just "changed" it to what it already was.
After a Restart of the Mac, those popup messages stopped. But I had to re-enter all my passwords in the Mail App for each of my four accounts.