I too have been experiencing a similar problem. I have been working with Novell and have an open incident. We have traced out the path of the "stuck" message that created the multiple messages in the user mailboxes to the MSLOCAL/MSHOLD/ <PO>Name directory. Usually in the #4 folder but could be in any one. By downing the MTA and removing the stuck message from the folder then restarting the MTA, everything passes thru for a while until the next time. In my case next time was Monday Morning I noticed that one of my PO had over 1000 mail messages in one user's mailbox. Basically the same procedure, shut down the MTA, go into the Domain/MSLOCAL/ MSHOLD/ PO folder and #4, sure enough their were several messages in this directory, however only ONE was file locked in the MTA and causing the multiple messages. One added note, If by chance the message that gets "stuck" is for a particular user, then only that user will get the multiple messages. However if the message was for multiple users, then all the users are getting the multiple messages.
This is where I am at this point. Still no perminant resolution. I'm GW 5.5.5 w/ NetWare 5.1.4