Build up of corrosion in the pipes, most likely. The well water probably has a high iron content and when water sits in the pipes it settles out. When you turn on a tap, all that corrosion gets washed out to the faucet. After the built up corrosion is washed out, the water probably starts running clearer, though it probably still has iron in it. A couple things: Have you seen iron stains on tubs, toilets, or sinks? If so, that confirms you have iron in your well water. You could also take a sample of water (that seems clear) and put it into a clear glass jar. Seal it and let it sit for an hour or so. See if there is sediment on the bottom. If there is, see if it reacts to a magnet. The last thing is to take two samples of water to your county extension or health dept for analysis. Take one sample when you first turn on the water (the first water that comes out) and then take another sample when the water seems to be clear again. Tell them you are looking to find out about the iron content.