Checking the Search hits so far, I'm seeing a lot of Blackberry hits and will address these in the coming week. I wanted to get started repopulating the site with something near and dear to my heart.
I have moved from working with a normal sized enterprise to one that is fairly large. One of my first major issues was investigating a situation where a client would stop "receiving" mail, although the router showed it moving fine. Later in the day, or maybe another day or so, mail would start to backup in the queue with the message "attempt to perform folder operation on non folder note" showing in the console (log file).
The short term fix was removal of the Inbox, refresh the design to recreate the inbox, then life would be good for a few minutes. The issue was reported to the support organization (you know which one). They started pointing to a duplicate Inbox, which in the long run, came to be true.
However! They pushed for an investigation to the design. It had to be in the design, they insisted to my recollection. Several iterations of the issue made the client every more insistent on a fix. (Amazing that our clients actually want consistent email, but that's another issue).
The issue revolves around the fact that the Router (apparently still so today) looks for a Note named ($Inbox). The Router doesn't look for a Design Note, just a Note. Don't try this at home unless you want to break things. Take a simple Note (message, todo, reply, doesn't matter), add a field named "$Name" and give it a value of "($Inbox)". Save to your mail file, and watch. The first phase, you will stop receiving new messages to your Inbox, and only see them in All Documents. Slowly (depending on the stream) you will start backing up messages in the mail.box(s) on the server. You will see the message "attempt to perform folder operation on non folder note" as the router attempts to deliver to the simple Note that you created.
So, the fix? Get a copy of NotesPeek, and search for $Inbox. Locate the Note, using the information provided (subject, recipients, etc.) Write down any recipients as they are most likely broken also. Remove the Note, remembering to remove it from the trash also.
Report the issue to support! Although they have provided a hotfix, and promised it fixed, I still see it in the wild.