I have three ref documents for you
https://learn.microsoft.com/en-us/azure/defender-for-cloud/defender-for-storage-malware-scan
https://stackoverflow.com/questions/60836786/scanning-for-malware-in-files-uploaded-to-azure
Microsoft Defender for Cloud's Malware Scanning feature performs scans when a blob is uploaded to a protected storage account. The scan is triggered regardless of the upload method, which means that modifying a blob (an upload operation) causes the modified content to be scanned after the update
If the scan is still not being triggered even after waiting for a considerable amount of time, it could be due to the configuration of your web app or the storage account. Malware Scanning depends on certain resources, identities, and networking settings to function properly. If you modify or delete any of these, Malware Scanning will stop working
As an alternative, you could consider implementing a custom solution using open source tools to scan each blob uploaded and download blobs only from a "clean" container
I couldn't find any additional specific configuration or settings you might be missing. If the problem persists, I would recommend reaching out to Azure Support for further assistance.