Driver side flowmaster at idle, while listening with stethoscope, has normal air rushing through it noise. However the passenger side flowmaster has a loud knocking sound, I tapped both muffler with a mallet and did not hear anything rattle around inside etc. Any idea whats causing this loud knocking through the muffler?

 

I never really felt the need to put a stethoscope on my mufflers.
I assume you were hearing something out of the ordinary to begin with?

Its likely that you have a noise in the valve train and it is transferred along the pipes.

 

possibly a broken baffle weld?

 

/Ding Ding Ding