I have experienced the same thing before.
It only seems to happen to me when I have included weighted dips in my workout program, which I noticed are also in the S-A program you are doing.
The process which causes the cracking or popping sound is called 'joint cavitation' (google it if you want to find out more) and is usually harmless. Since you said that it causes you no pain, and if you have no other accompanying symptoms, I would not think that it is anything for you to worry about.
However, as already mentioned, some soft tissue work in the thoracic region may benefit you, if you are not already doing so.
Here are a couple of articles from my favourites list that you might find useful...
Soft tissue work for tough guys:
Feel better for 10 bucks: