I hate to add to the list of issues but I got a couple of auto-payout emails this morning but nothing is pending on those wallet addresses. Can't get into the website to see what it says but the coins paid out were close to my threshold so that much seems about right.
I've noticed a similar issue - recent auto-payout of MEC not showing up in my Cryptsy wallet.. but if I look at the blockchain explorer
http://mega.rapta.net:2750/chain/Megacoin I see it listed there.. I actually experienced this a few times in the past.. it seems that some wallets on Cryptsy don't show pending deposits until confirmed.. Not sure why, but you may want to check separate blockchain explorers for your coins to get an idea.
In any case, the multipool website/frontend has been up for me all morning so far (UK time).