Perhaps I am wrong, but I thought that turning individual plugins off did more of a mute of the output of the plugin than it really turned them off.
 
Bob Bone
 

Hi drewfx1
 
I agree that I can be the victim of my proper imagination; how many times, I turned a button on a plugin or on a device, and I litterally  could "hear" an effect whereas the plug or the device were turned off !!
But I systematically check more than 2 times because I'm very scrupulous concerning the sound; 
As I said, I have to go deeper, but I could confirm that the signal wasn't the same and maybe this is under particular circunstances that I have overlooked.

Hey Robert,
Maybe this can be an explanation !!  That would induce that the signal should pass through the individual plugins and turning them off would attenuate the signal !
 

That is definitely not the case. Turning it off bypasses it.

SOME plugins still allow signal through them even when turned off.
 
You might also try stopping and restarting the audio engine after turning plugins off.  That has been reported in the past as helping clean up sound after turning plugins off.
 
Bob Bone
 

I have never had a plugin mute sound when using the Sonar bypass. Could you point me to one?

Additionally, the OP said his sound got "clearer and more dynamic", he didn't say there was no sound and then there was after hitting the switch.