Hi,
Since I switched to Sierra, I keep getting the message that "NetAuthSysAgent wants to use the "login" keychain".
Thus far I have created a new login KeyChain, but the message still pops up.
It may be related, but I have a script that mounts a few NAS shares (using AFP) on my desktop, and it is in connection with these that the message pops up. I am asked the password, eventhogh it is saved in KeyChain.
Apple really has to sort this out before releasing Sierra. I have a few few hundred Macs where I have a mounting script going to attach shares...