From my understanding, when you send a script from within Amazing Charts, it doesn't get sent right away. It goes to newcrop/surescripts first then to the pharmacy. I have noticed on multiple occasions there is a delay after I send the script. On the other hand, I've had a patients cell phone ring with the pharmacy calling while the patient is still in the room.
In my humble opinion, when the pharmacy tells the patient they haven't received the script, more often then not they haven't really looked (or it's just too early after the script was sent).