I just traded LTC for BTC and was able to withdrawal instantly. You need to email btc-e and let them know about the problem. I can email them for you if you like. It says this on the front page of btc-e.
Our advantages:
Trading in automatic mode.
Addition USD deposits within 24 hour
Instant deposit/withdrawal all coin
USD Withdrawal within 72 hours
I opened support ticket, but the automated response said it could take 72hrs. I think I am just hosed.