Ok well first thing is that the clearCache function that you have mentioned is only for the local cache the web client stores (I think).
I thought that I had seen your problem before on the forums, unfortunately it was
your other thread detailing this problem. I took a look around and found this wiki entry:
Zimbra Directory Service (LDAP) - Zimbra :: Wiki.
Could you take a look at the attributes listed there on one of the accounts that shows up twice and see which one is possibly causing this?