Nick, can you try this and see if it resolves the issue?
For each SVM
1. Turn off quotas
Ex:. cluster::> quota off -volume <volume_name> -vserver <vserver_name>
2. Add one default quota rule of type 'tree' on each volumes hosting SMB shares.
Note: If one already exists, this will fail, which is an expected behavior and fine.
Ex: cluster::> quota policy rule create -vserver <vserver_name> -policy-name default -volume <volume_name> -type tree -target ""
3. Turn on the quotas for that volume and restart SMI-S agent.
Ex: cluster::> quota on -volume <volume_name> -vserver <vserver_name>
{wait for job to complete}
Ex: cluster::> quota show -vserver <vserver_name>
Please let me know if that does the trick.