I have 2 users now the same issue: since upgrading to 6.5.2 when they select a mail to be deleted from the inbox other unrelated mails get deleted, these other mails are not even the one next to it but maybe several mails away.(soft deletes are on with 48hrs)
Any one seen this one?
Ta Matt
Subject: Wrong emails being deleted
Could it be that you have customized the template in some other way eg. You have a script that moves marked documents out of the current folder, this means that the are still selected but in the background. When user hits delete all selected documents, including the ones marked in the front, end up in Trash.This does not always happen but it could happen depending on how the script moving document is written.
Subject: RE: Wrong emails being deleted
I just remembered that this was with R5 client not ND6, sorry
Subject: RE: Wrong emails being deleted
Sounds like a good test of the backup system! 
When strange things like this happen, we usually run maintenance against the mailfile: compact, updall, and fixup.
Also, a quick ctrl-shift-F9 to rebuild all view indexes sometimes does the trick and is a good first step.
Good luck!
Subject: RE: Wrong emails being deleted
Cheers Paul, The list of things I have tried is long but distinguished. everything for fixup to compact -c, deleting the rep on that server then pulling back from another. For one I gave up and gave him a new mailfile, then the next day got told it has happened again!Matt