Benjamin,
I know you had mentioned that your permissions on the SmarterMail directory are wide open, but could you please confirm that the account that's handling the SmarterMail application pool within IIS (this should be Network Services based on our documentation) has full control over the MRS directory (default C:\Program Files (x86)\SmarterTools\SmarterMail\MRS).
We do have a thread that will go through and clean these items, and we have confirmed this is working in our test environment. If your permissions are set correctly, I would strongly advise opening a ticket with our support department so we can work with you further to isolate the issue and come up with a fix.