we have exact the same issue on Domino 6.5.4 (clustered). replicate unread marks is enabled and usually the read/unread status is updated correctly. It only goes wrong when one of the 2 mailservers does down for work/full backup. We reported this to RIM, here is the answer:
This issue has been investigated by our Software Development Team and they
have now created SDR68366 to further investigate and resolve this issue.
The following update was received:
In speaking with Lotus, they indicate for the most part it should work with
the data available in their technotes, however, for us to fully address it,
we would need to use a new APIcall that is not available until 6.5.3. That
would mean for us to be able to use it, the BlackBerry Enterprise Server
would need code changes as well as run on a 6.5.3 or later server. They have also indicated that the BlackBerry Enterprise Server updates the
unread table, rather than the activity log.
Currently the fix for this SDR is scheduled to be fixed in
Release 4.1.1. of the Domino BlackBerry Enterprise Server. As yet we have
no definite time frame for when 4.1.1 will be released. Hopefully we are
looking towards early / mid 2006.