Using configImport on application startup doesn't activate all settings

I am using Azure Key Vault to store by CFConfig file. In onApplicationStart I connect to the vault and get the contents, deserialize them, and call configImport(). Looking in the admin UI, I can see that some settings have been activated, but not all. None of the scheduled tasks are present, for instance. If I restart the engine from the admin, then all of my settings show up. I use flushExistingData=true in the call. Is there anything else I should do or does this sound like a bug?

Using the official Docker image: lucee/lucee:
Admin extension