I might have had a similar experience earlier today.  I think that there is some error occuring and you will need to manually enter a MtGox Code.  I've heard people saying that their Account Number changed recently, and I have a suspicion that it might be related to that...just a guess.

You said that you received the confirmation email.  Mine had a line starting "APIResult".  The string after that started as MTGOX-USD-a-bunch-more-characters.  I did a copy-pasta with that string into the MtGox code box and funds appeared.

Good luck!