Why would a transaction take 90 minutes to get confirmed?
Bitcoin has longer confirmation times than many altcoins like Litecoin or Dogecoin, and different services make their own choices about how many confirmations to require before a deposit is made available for use.

While you can see a new transaction on the network almost instantly, many services require six confirmations to prevent double-spending.  With Bitcoin, six confirmations will commonly require an hour and perhaps more if no transaction fee was added.

Given the description, it leads me to believe that Cryptsy wanted to see six confirmations before making your deposit available to you on the Cryptsy site. It's not really unusual to see that take the 90 minute wait you experienced.