Hi,
Dont turn both tabs on in bitstamp! One api per currency pair, there is only one pair at bitstamp. You will overload the api and get banned. Yea there are issues with bitstamp sometimes, I am not 100% how to solve them. Check the "support" tab at the bottom and see what it suggests.

I think all the problems with cryptsy are on cryptsy´s end and not the bots.