I had a steel Trek 850 MTB back in the 90's that had this same problem on the rear triangle.The rear wheel was a good 2-3mm off to one side. I just rode it, but it always bugged me a little bit. It was more noticeable with rim v-brakes, because the arms would be angled to one side and not symmetrical on the wheel. I always suspected that the frame got bent somehow, but there were no obvious signs of damage.
I've never noticed this issue on any other bikes I've owned. Even my Cannondale SuperX with the 6mm "ai offset" still has a perfectly centered rear wheel (ok... nothing's perfect, but <1mm). I did try to slot a regular dish rear wheel in there out of curiosity, and 6mm is a pretty big offset.