Is this new behavior with Microsoft AutoUpdate? Did it work for you with earlier versions?
When setting this with a script through Jamf Pro, the script is going to run as root. You'll need to use something like Jamf's $3 variable, which substitutes the current username:
defaults write "/Users/$3/Library/Preferences/com.microsoft.autoupdate2.plist" HowToCheck -string "Manual"
or
su "$3" -c 'defaults write "/Users/$3/Library/Preferences/com.microsoft.autoupdate2.plist" HowToCheck -string "Manual"'
Either of these commands must be triggered by the user using something like a Login trigger from a Policy or a Self Service policy while the user is logged in to Self Service.
A configuration profile is easier to implement. Edit a copy of your com.microsoft.autoupdate2.plist file to keep only the HowToCheck key and Manual string. It'll look like this:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>HowToCheck</key>
<string>Manual</string>
</dict>
</plist>
Upload that to a Custom Settings payload in a new configuration profile and be sure to apply this to the Computer level under the General payload. After saving, click the Download button at the bottom of the configuration profile to download the .mobileconfig file and allow it to install on your Mac. Relaunch Microsoft AutoUpdate and verify the settings.
