You might also be experiencing a problem with not having the right strategy in Auto/strategic combat. Some of the strats don't target missiles, or even fighters. You may have to choose or make a different strat that will take care of the treat. In CB it is the use of specialized ships to fill specific roles.
These guys certainly know what they're talking about
One thing to note is that you should not expect PD ships to be as powerful as in stock. They help reduce damage, but even a giant fleet of PD ships will get pegged by a missile or two every now and then.