I don't have any problems since 2 days. All trading actions are handled within less of a minute. Sure - it should work instant but compared to last week this is now much better.
Im the same, have transferred and sold 900mil CENTs today without problem.
moved the income to NETcoin and replaced a sell order. All is working as it should.
Cryptsy has never been the fastest exchange but it gets there in the end.
I did end up losing 0.16 BTC from a sale and waited 28 hours for a response from Support which was them saying could you please provide x/x/x data (even though it was all in the first ticket!) I did comment saying they would get through tickets quicker if they read them and then act rather than doing a standard copy and paste of a time waster message. (because they didn't fix the issue I had an additional 9 hours wait {they replied just after i went to bed!})
anyway a couple of hours later the BTC arrived in my account safe and sound (I have also received some additional coins which would of appeared to have gone missing months ago! not massive amounts but it seems as though the Audit they ran has resolved a lot of the missing coin issues.)
So if you want to be a second by second trader i would avoid Cryptsy at the moment.
if you want to buy at a set price and then sell at a set price Cryptsy is great.