I had an issue with some DOGE that dissapered on Cryptsy, however around 1AM EST today, it seems the people @ Cryptsy did a DOGE coin wallet update or fix. My funds re-appeared and are 'usable'. From what I have been told by very knowledgeable people that have been doing this a long time is, that after many transactions the wallet.dat of ANY coin gets very large & laggy & needs to be 'rebuilt'. Just imagine this on the scale of what Cryptsy does hourly, or even daily, especially in light of the recent DOGE volume. I hope your problems gets resolved soon, as I know it can be frustrating.
They make .5% BTC on every sell/buy... the volume... they can afford to have a staff 24/7
Even better, at least let the public know that your doing something... not just let it be broke, and then inform people "O BTW we finally fixed it ".