Corrupt Apple Keychain in OSX 10.11.6 after Security Update 2016-003

Not sure if it was directly related to the installation of Security Update 2016-003, but very soon after that installation I started having trouble with accounts on Apple Mail. All of my email accounts are Google Apps or Google Suite accounts, or just plain Gmail accounts. All of them went offline and entering their passwords would not restore access to them.

When I went to System Preferences –> Internet Accounts and entered a new password, it accepted the password but on the screen where you select which parts of the Google account you want to sync the Done button was greyed out and there was no way to get past this screen:

I went to Keychain Access and tried deleting everything related to Google, then tried deleting all of the keys and continued having trouble. Some online guides were recommending resetting the password for the Login keychain:

That didn’t appear to do the trick for me either. The only thing that would finally work is if I went to Keychain Access –> Preferences –> Reset My Default Keychain:

Then I went to System Preferences –> Internet Accounts and re-entered the passwords for all of my accounts, this time when I got to the Google window where I was stuck before I could select the items I wanted (Mail, Calendars, etc.) and the Done button wasn’t greyed out and I could proceed normally.

I’m guessing the keychain got corrupted in some way, possibly when the security update was applied. I did attempt just restoring the Keychains folder from Time Machine and that did work (I still had to re-enter some passwords) but I didn’t really want to revert to and older backup and kept working on various solution attempts.

My other thoughts for the possible cause were incompatibilities with GPG Mail with this version of mail after the security update, but I was able to re-activate that mailbundle and it has no problems running.

I had also attempted the solutions from this thread: Can’t login with Google using Internet Accounts

But I needed to do a larger reset than just deleting the Google keychain items.

Many of the threads I was reading kept referring to Apple’s Keychain First Aid but that functionality was removed with the 10.11.2 update and it appears there is no current alternate tool for it. Some mentioned that running Disk Utility would fix keychain problems and I tried it but had no luck getting it to update anything. I don’t think Disk Utility really verifies or repairs broken keychains.

More information on that topic can be found here:

Were you having the same problem with your Google accounts in Apple Mail? Did any of these solutions help you or did you find other solutions that worked for you? Please let me know and share the info with anyone else who stumbles across this issue.