The wood used for your home's siding may contain water-soluble extractives. Water-soluble extractives are found in the heartwood of both soft and hard woods. Moisture causes the extractives to be leached from the wood and they then interact with the paint, typically leaving stains that are red and brown in color. Prevent stains due to water-soluble extractives by applying water repellent to the wood before it is first primed, then using a stain-resistant primer. Fix the problem by cleaning, re-priming with a stain-resistant primer and repainting. Any areas in the structure of the home, such as exposed siding seams where rain, snow or dew are able to be absorbed into the wood, also need to be sealed.
You may think of mildew as being green, but there is also red mildew and black mildew. Mildew, which is produced by fungi, will likely occur on parts of the house where moisture accumulates and where there is less open air. Identify mildew by observing its spores under a magnifying glass. Eradicate mildew by cleaning the affected areas with a solution of 3 quarts water, 1 quart bleach and 1/3 cup detergent. Repaint using oil-based primer and paint that has mildewcide. For extremely damp climates, use paint that also contains zinc oxide.
Blue stain is another product of fungi that can occur when the wood is exposed to moisture. It will cause blue and black discoloration. Prevent blue stain by making sure there are no areas where rain, snow or dew is able to penetrate the wood. Make sure all siding seams are sealed, there is no peeling paint, you have an adequate eave and gutter system, and there are no places where water can pool up against the house or on the roof. Prevent blue stain by applying water repellent to the wood before it is first primed, then using a mildewcide primer and paint. Fix blue stain by stripping the paint, drying out the wood, applying water repellent and repainting with mildewcide primer and paint.
If non rust-resistant nails were used to attach the siding to your house, reddish stains can occur around the nail heads. Repair rust stains by removing the old nails, cleaning the rust with a rust-remover solvent, rinsing the solvent with fresh water and replacing the nails with rust-resistant, galvanized, stainless steel nails. Countersink the nails, caulk the nail heads and repaint over the nail heads.