Its probably a combination of factors
the pump probably triggered loads of users holding the coins in wallets on their computers to sudden deposit and caused a huge backlog.
something else to consider is the speed of the network of the particular coin - If a pump has happened and suddenly everyone thinks wow i should mine that coin! the difficulty suddenly goes through the roof, people realize its not profitable to mine with the difficulty so high, the hash rate plummets as people stop mining and move to another coin and you are left with only a few miners trying to confirm the blocks at a huge difficulty. which then slows the network down and confirmations etc
I personally don't think they are showing favoritism to anyone, after all if a miner dumps loads of coins Cryptsy gets the same cut of the profits as they would if it was a trader selling what they already held on the site.
In my case i did the deposit before the pump start and before Skyrocket, talking about FST, and the network is moving around 250Mh-400 peak so far, now about his speed hell is fast 48sec,
Its now 12hrs!!
Miner is dump once, trader is buy n sell & repeat doesnt sound to me like the same cut , and if new deposits dont come in the price will stay high longer.
you still believe they dont shown favoritism to anyone
Miner
Dump move on to next coin
Dump move on to next coin
Dump move on to next coin (I could keep typing but im sure you get the idea.)
Without the miner dumping the traders have nothing to trade.
It sounds to me like you have a problem with your specific deposit, no one else is currently saying they have the same issue (at least they haven't mentioned it in this thread)
has it actually showed up in the block explorer?
Sorry i cant actually be any real help was just throwing in some suggestions which might not of been considered ;-)
and i still believe there isn't any favoritism being shown, otherwise there would be a massive fee on the Auto sell option to screw over the miners.
also at the end of the day when you get your coins back (and im 99% sure you will, I haven't heard of a case where Cryptsy has actually lost them!) you can always withdraw them and then never go back. Its totally up to you in the long run ^.^
I wish you luck with your search for your coins ^.^