Currently I still use both 1Password versions (4 & 6) parallel. I noticed that the auto update always enables the automatic start with Windows option after an update. It would be nice if auto update doesn't touch that setting. I am also not sure if auto update overwrites any other settings with default values.
The setting should stay untouched during each setup.
1Password Version: 1Password 6.6.406d
Extension Version: Not Provided
OS Version: Not Provided
Sync Type: Not Provided