I've seen a situation similar to this... one of my local hydro shops was sporting a large ebb & flow table right in the shop's front window with six tomato plants (trees, more like) flourishing underneath an air-cooled, 600W HPS lamp. There was no hydroton in the table, only in the 10-inch mesh pots which housed the plants. The roots were spread across all four corners of the table and the mat was at least an inch deep. The roots themselves ranged from medium tan to dark brown.
I asked the guy who runs the store about this, as the plants themselves were obviously quite healthy and were fruiting bountifully. He explained that the intense exposure to light was causing the discoloration, as was the particularly dark nutrient bath he was using. He pointed out that none of the roots were fuzzy or mushy, so while they didn't look argent at all they were certainly healthy. Other than a few bugs eating leaves occasionally, the plants completed their life cycles without any problems whatsoever and produced several pounds worth of fruit.