what headphone amp are you using? Either its bad, or you're sending too hot a signal to it. The input should not be coming from a headphone out. That out has a little amp in it already, which may cause the headphone amp to distort.
About the latency, it all depends on how you are monitoring. If it's straight out of the 001, you have to set the latency REALLY low when you're tracking in Pro Tools. I prefer external monitoring through a console myself rather than through the software.
H2H