Assuming that reconciliation settings are
set correctly on the handheld and on the BES server for this user, I'd suspect the state datebase first, then once you rule that out, I'd look at the mail file itself (run the fixup, updall -R, and compact utilities against it - failing that, try taking a new replica or a new copy of the mail file, or reapply the default mail template).
does this user have a lot of documents (>1000) in his/her Inbox view, or does he/she have a lot of folders/views in the mail file?
but these are just wild guesses. Sync Problem Read/Unread messages Lotus Notes personal folders Attachment Error on 8700 G