The stains you see are from corroding or rusting nails and fasteners. Cedar mills recommend the use of aluminum, stainless steel or polymer-coated fasteners. When galvanized nails or fasteners are used in Cedar, the acids in the wood react with the zinc and cause the corrosion streaks you see on your fence (see also why Cedar). At first, the only sign of fastener deterioration may be the streaks, but eventually the fastener will decay enough to lose its friction hold in the wood. Then your great-looking fence begins to fall apart.