I have the same problem with my 90mm when used in the portrait orientation, and especially with the lens hood on. It took me a while, but I figured out that the problem was the moving part of the lens is a little loose, and it rubs against the stationary part as it focuses. The friction causes lots of vibrations and noise. At first, like you, it seemed intermittent, then after lots of fiddling I discovered it only happened on it's side (portrait orientation) and with the lens hood on (because it weighs it down). Without the lens hood it does happen, but it's hardly noticeable.
I found that if I lightly support the moving part of the lens with the tip of my finger as it focuses, there is no noise. Unfortunately when I sent the lens to Contax for repair they sent it back saying "No problem found" even though I clearly described the problem in my paperwork. Kinda sucks because I hardly use the lens now, and that is the main reason.
I was thinking of sticking a very thin piece of tape of some sort on the rubbing part, some kind of tape that is very smooth, and that should help, but I don't like the idea of having to use tape on my beloved G equipment.
I had posted this question to the Contax G Forum a few months ago, and was surprised to hear that there were a few people out there with the same problem. I guess it doesn't get worse, because they didn't seem to mind it once they were used to it. Unfortunately, I think that the strong vibrations in time could start to do damage to other parts of the camera...
-Vu