Message remains in spool after expunge

[Arnaldo Viegas de Lima]

Hi,

We have just migrated from 2.4.17 to 3.0.3 and we are having a problem with one of our scripts that perform actions on a SPAM folder for retraining purposes.
All files placed by the user there are used for retaining. At the end Cyrus is called to remove the files: we mark all files for deletion and then expunge the mailbox. We have been using this script since 2007, flawlessly. 

I’ve set Cyrus chatty mode on and I can see the commands being sent to the server and there is a confirmation log message for the expunge, with the  correct number of files.
Checking the SPAM mailbox with Cyrus (or any IMAP client), show it as empty. But looking at the mailbox directory in the filesystem, the actual files are still there.

Am I missing something on 3.0.3 that may be the cause for this problem?

Thanks in advance.

Arnaldo.