Credentials popup keeps popping up after El Capitan upgrade
I've received the answer to my problem from finchr's post at https://discussions.apple.com/message/29270520#29270520,


  In my case the problem was with MagicPrefs, a utility that lets you define additional mouse and trackpad gestures.  Disabling MagicPrefs allows Keychain to see Allow/Allow All mouse clicks.


Which was the very same for me.  I haven't permanently disabled, or uninstalled MagicPrefs, I just disable it when I need to click one of those boxes.  Hopefully they or Apple will come out with an update that fixes this.