Not sure if you already figured this out but I faced this exact issue the other day. Is your Xcode build box remote? Is ARD/VNC enabled? Apple recently released an update for CVE-2015-5943 'A malicious application can programmatically control keychain access prompts' that made it so the always allow/allow buttons didn't work is VNC/ARD is used. The other thing that can cause that error to come up is apps that modify system input like Smoothmouse or MagicPrefs.
You can get around this by re-importing the private key and trusting the codesign binary on import. If you don't have the original private key .p12 file, you may be able to export it from your Keychain. You'll want to remove the private key from the keychain before reimporting (make sure you have the private key backed up somewhere first!!).
To import and trust the codesign binary, you can use this command.
security import /tmp/my-cert-path.p12 -k /Users /xcodeuser/Library/Keychains/login.keychain -P mysupercoolprivatekeypassword -T /usr/bin/codesign
If you need to keep adding trusted apps to the private key, I would definitely make sure to keep your developer private keys backed up elsewhere from here on out. If you lose the private key and cannot export from Keychain Access, think you may need to regenerate it if you don't have local access to the box (we use a remote hosted Mac Mini).
The log entry you posted is the correct one.
SecurityAgent[1476]: Ignoring user action since the dialog has received events from an untrusted source
'About the security content of OS X El Capitan 10.11.1, Security Update 2015-004 Yosemite, and Security Update 2015-007 Mavericks'
https://support.apple.com/en-us/HT205375
Other folks facing same issue:
El Capitan + Xcode 7.1 not letting me allow enterprise signing
https://superuser.com/questions/1004881/osx-10-11-1-keychain-access-does-not-allow-change-to-access-permission
http://nerdanswer.com/answer.php?q=1181710