Cryptsy has been having some overload issues the past couple weeks.
I had a similar issue, sent some btc to my cryptsy account and it never showed. Looked in blockchain and it had 65 confirms then.
I contacted support and that is when they told me about the issues. They told me to check it in 4 hours and if nothing to contact them again. I ended up going to sleep and it was there in the morning.
All I can say is keep with support. As long as you can show it went to your cryptsy address you have a case. If your client had a fork issue when you sent it, you might be sol
Thanks for your reply. How do I know if my client had a fork issue or not? (it has over 6000 confirmations if thats relevant).