This was very painful to resolve, but, hopefully, this will help someone else in the future.
We had an end user who was receiving new email messages in his All Documents view but they would not show in his In-Box. We tried all the usual things we have tried in the past when this happened: Copy the inbox contents into a temporary folder; delete the $Inbox design element; refresh (or replace) the design from the template; run updall -r; run fixup; run compact. The fixes only lasted a few minutes. I finally copied his mail file to my workstation and created a brand new mail file on the server for him and copied his messages back into the server copy. That didn’t help either.
We finally noticed messages on the server console:
Unable to add note 46DE to folder in Database i:\lotus\domino\ourserver\mail\hismail.nsf: Attempt to perform folder operation on non-folder note
We know when the problem started, so we started looking at the document properties of the messages in his mail file from that point on. We found one document with about 60 $ There were several that were $scriptobj_xx and one, in particular, had a field called $ClassName with field contents of “Folder”! That particular message appeared to be masquerading an “inbox” and therefore, new messages could not go into the $Inbox folder.
We deleted that message (which he actually sent to someone else) and immediately, several pending messages showed up in his inbox! We ran the updall/fixup/compact maintenance and things appear to be working correctly.
Hopefully, this may help someone else in the future.