Messages moved from Inbox to a folder on one replica remain in Inbox on another replica

Notes 6.5.4 client, upgraded from 5.0.13 several months ago.  User runs on a laptop and was happy as a clam until a month or so became apparent that the user's local replica and server replica were not in sync, based on three issues:  
1.  one or more documents which were 'stuck' in the inbox of the server replica, and attempts to open the doc resulted in 'invalid or nonexistent document'
2.  other documents in the inbox which had been moved into folders on the local replica still showed up in the inbox of the server replica
3.  occasionally some messages would not show up in the Inbox but could be seen in All Docs (no clear understanding as to when or why, though)

To help address these issues, user verified local replica was current and behaving properly, and the server replica was deleted, then the user replicated up.  We kinda figured all was well - no more invalid docs, no more docs missing from the Inbox.

One problem remains, though.  User spent some time getting server replica all organized and filing the Inbox messages in a number of folders.  These changes are not reflected on the local replica, though.  Deletes and (most) unread marks are updated properly, but the folders thing isn't, and the user is pretty frustrated.

Tried removing the local replica and creating a new local replica (including deleting the nsf file and the .ft directory).  Tried ctrl-shift-f9 on both sides.  Seems like a silly problem but it won't go away...
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Sjef BosmanGroupware ConsultantCommented:
Domino version?

Maybe you should make a fresh replica of the right database on the other system.

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Also, I would replace the design on the server. Is the template a standard  R 6.5 Mail template ?

I hope this helps !
Question, other than replacing the design, did you delete the replication history on BOTH the server and local replica?   Go to database properties, delete the FT index, then go to replication settings and delete the history.  Then try replicating once more.
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bconreyAuthor Commented:
Sorry to be slow in responding.

Tried replacing the design on the server's replica of the mail file, to no avail.  Mail template is the standard 6.5 template. Tried deleting the replication history on both server and local (including FT index, as suggested).  Unfortunately none of the things I've tried nor been recommended seem to resolve the problem.

One thing I learned from the user, though - It only happens on older documents, more recent docs end up in the folders they're supposed to be in.  Based on that, I had the user organize their local replica (as they'd done with the server replica) and let it go for a day or so, and confirmed everything (new) received and moved into a folder on the local replica is reflected on the server replica.  Since this isn't an epidemic, it probably doesn't warrant too much additional investigation.

Thanks for responding, though; I've upped the points so I can split them between you.
Thank you for the points.. I only wish we had a solution or at least an explanation for you.
Sjef BosmanGroupware ConsultantCommented:
Maybe this: look in the Replication Settings of the database, click on Other. Look at "Only replicate incoming documents ... after". The documents not replicated, are they from before that date?
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