Sounds like a logic bomb, intentional or otherwise.
I know in some parts of Orion (NCM I believe), I saw similar behavior and at times used service accounts to create alerts and NCM jobs as a workaround.
Looks like a known issue with a known fix:
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what you describe is designed behavior (as far as I remember), however I confess this can be misunderstood.
Alert conditions are always evaluated under the owner account. This causes also application of the owner's account limitations. In other ways - objects, which the owner can't access, won't trigger the alerts. This way you can e.g. target the alerts to specific users. Bad is, that if the account is disabled, the alert conditions can't be evaluated as the owner can't access the queryengine and besides the logs I'm affraid this is not visible :-(
To resolve this, you can:
- Change the owner to existing account
- Set NULL to CreatedBy field - when this is set to NULL, not-limited system account is used here. (update alertconfigurations set CreatedBy=NULL where CreatedBy='mydomain\BadUser')