And also just to add, from memory I had the issue when I moved faders by mouse or controller. I'm convinced it was a graphics glitch somewhere.
 

I know you tested it without the graphics card present, but I am unclear as to whether or not you also explicitly disabled the video drivers and then tested.  I am wondering if they would have still loaded unless explicitly disabled.
 
Bob Bone
 

Graphics yes because even with midi the graphic fader image moves. This is what I was talking about too. Any movement on the screen made noises with that one set up I had. It didn't come though on the recordings so I just ignored it. It could be only recorded by using "what you hear." 
 

There is a parameter in aud.ini called "MixDezipperUsec". Any clues in the manual? (E.g. "Setting MixDezipperUsec too low can cause clicks while rendering abrupt gain changes due to envelopes.".)