well, I always had that problem with a lot of users including me.

my handheld is entreprise activated since few month (I've changed phone )

let's say today
few email are still set to unread on handhelp as I read them on my local outlook. Even if I force a reconcile now "few" don't sync

wireless message reconciliation is enabled

but hard deletes reconciliation is set to false...
I don't understand of this last option, maybe it can help me ? Even if I try to synchronize with the desktop manager, it doesn't change anything