Main Bose Amp for door & rear speakers is in trunk on driver's side. Sub amp is located in the compartment with the sub.

 

^ is your antenna wire in all the way?

 

OP I have the same exact issue in an 04 Touring with Bose/Navi.
ONLY happens when using CD player.
Radio works 100% fine, and tape does as well (AUX In mod for tape, anyway).

As previously noted, I agree that it is an issue with either the internal disc changer, or the ribbon between the internal disc changer and the rest of the head unit.

I am going to be ripping out the entire Bose system in the next few months, and I might have a look inside the head unit and see if anything appears to be loose.

 

RE>:"Need help troubleshooting : Losing sound on one side."

Isn't that a known problem with the Z's Bose H/U?

From what I remember, replacing the Bose H/U fixes this problem (even when it's specific to the CD player).

--Spike

 

I have the same problem
04 roadster, randomly cuts out.
Really annoying.

 

I had an issue with my driver side speaker cutting in and out on my Touring only when using CDs. I fixed it by replacing the HU.