I have exactly the same problem, but with sending Bitcoins from my local wallet to Bitstamp.
When I send my Bitcoins to Bitstamp it immediately showed as an unconfirmed transaction, waiting for the 3 confirmations.
After 2 days when the 3 confirmations were received (according to my local wallet) the Incomming transaction dissapeared in my Bitstamp account and my bitcoins are not added to my account.
Looks like they 'dissapeared' while the transaction is fine according to blockchain.info. Send in ticket through the support function 6 hours ago, I guess I'll have to wait a bit longer