Office 365 Outlook prompts for password

We have a deployment of Office 365 with ADConnect SSO enabled. Additionally, with the implementation of modern authentication (MA) we have set the flag to true. https://support.office.com/en-gb/article/enable-or-disable-modern-authentication-in-exchange-online-58018196-f918-49cd-8238-56f57f38d662

We also enabled MA for Skype online even though we do not use it fully currently.

https://social.technet.microsoft.com/wiki/contents/articles/34339.skype-for-business-online-enable-your-tenant-for-modern-authentication.aspx

More info on Modern Authentication:

https://support.office.com/en-us/article/using-office-365-modern-authentication-with-office-clients-776c0036-66fd-41cb-8928-5495c0f9168a

We started seeing issues where Outlook would prompt for password, especially after password change. After much searching we found the following reg key that is recommended by MS when MA is utilized in order to force outlook to use MA.

https://support.microsoft.com/en-us/help/3126599/outlook-prompts-for-password-when-modern-authentication-is-enabled

https://support.microsoft.com/en-us/help/4041439/modern-authentication-configuration-requirements-for-transition-from-o

We deployed the keys with GPO Preferences.

Outlook:

HKEY_CURRENT_USER\Software\Microsoft\Exchange\AlwaysUseMSOAuthForAutoDiscover

Dword: 1

Skype for Business:

HKEY_CURRENT_USER\Software\Policies\Microsoft\Office\16.0\Lync\ AllowAdalForNonLyncIndependentOfLync

Dword: 1


Update: 
We've had a few users where this issue started again. 
Settings - Accounts - Access Work or School - select user - disconnect.  Fixes every time, instantly so far.