MacOS – Yosemite causing problems with Keychain

The problem is solved. Unfortunately I've done so many things that I don't know what solved it.

Here are some things I did. These steps should be safe but in any case before starting either make sure your time backup is on and/or make a backup of your Keychains folder in ~/Library:

• Remove / re-add the keychains
• I disabled iCloud and re-enabled it again (and rebooted in the mean time) (I suspect this was part of the solution)
• I cleared Safari history data (although I'm pretty sure this didn't have any effect)
• I toggled the Safari preferences to remember passwords (for sure this was not the solution but might have helped in combination with iCloud reset)

Some things I did but where you should be a bit more cautious about:

• In ~/Library/Keychains: I deleted a folder called F1090786-29BB-5136-A02B-7266FEF0DD9A (actually moved to tmp location) (found somewhere on the apple community sites)
• I removed ~/Library/Preferences/com.apple.security.plist (again: I actually moved it away)

The "admin" account you set a password for was "System Administrator (root)". You'll either need to type "System Administrator", or "root" as the user name. This "super user" account is part of the operating system, and can do whatever it wants - including things that have extremely negative consequences. I recommend disabling it. See OS X Mountain Lion: Enable and disable the root user^[1] for how.

If you want to fix the keychain and can't figure out what password it uses, open Keychain Access and click the "Reset my default keychain" button on the General tab of Preferences. If a problem with "Local Items" occurs after rebooting, see this article.

As for the use of empty passwords, that is probably on purpose. You can't start a new user with no password anymore, and you can't unlock Security and Privacy system preferences without a password.

And finally, Chrome doesn't have a keychain to make use of on other operating systems, so if it can't use the user account's keychain it makes sense to me that it'll fall back on its own internal storage.

^{[1] It has been the same method for a long time, you can ignore the "Mountain Lion" in the title.}