I have the opposite problem. Works from scheduled search, not from the script.
By adding debug to sendemail.py I can confirm that when running from sendemail, it doesn't pick up the config that was set using the GUI. When running from scheduled search, it does.
Strangely, I have two saved searches - one uses a value for action.email.mailserver from users/ben363/search/local/savedsearches.conf. The other saved search (same file) doesn't have that value - it uses the value from system/local/alert_actions.conf
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