If you use the old message format, here is my patch in the 3.6 forum that gets rid of duplicated messages:
https://vborg.vbsupport.ru/showpost....&postcount=953
By 'cron' do you mean the Scheduled Tasks in vBulletin? The Scheduled Tasks run only when the forum has some activity. You can run a PHP command line (CLI) script and schedule it to run every 5 minutes by using the real cron (crontab), or Windows Scheduler, depending on your operating system. The script is in this post:
https://vborg.vbsupport.ru/showpost.php?p=1581411&postcount=898
If messages do not get deleted, have a look at this post:
https://vborg.vbsupport.ru/showpost....&postcount=886
All these patches are used on vB 3.8.4 with two mailboxes.