We get black flakes in all our hot water (all copper piping). Every faucet, shower, tub, dishwasher, etc... I've replaced the hot water tank (w/ anode rod completely removed), shocked the well twice (I still get similar looking sediment from it), and added a new backflush filter (to the current setup of inline filter, softener, carbon filter). I still get the flakes. I've flushed the new hot water tank numerous times, and had a large nozzle place on it to remove any larger sediment. In draining the hot water tank, I always turn the gas to pilot and have experimented in drain all hot water to selected faucets. I still get black flakes in the hot water... What is next? Pipes? I can't really explain why is it just in the hot water. The well water does contain similar looking sediment - but I can't figure out how it would get through two filters.
My first thoughts are:
It sound like you have iron sediment built up in your pipes, usually caused by by the iron pipes. You say you have copper piping inside the house. Chances are you have steel piping going into your well.
I reccomend you replace those sections with plastic piping.
My second thought however, because you have filters:
I have seen dip tubes from water heaters disengrate and this would answer why only the hot water side.
To check this, disconnect the water heater adn pull the dip tube out. visually inspect it.
My Third thought is build up in you pipes of iron before you put filters in will take some time to flush out.
With out seeing the set up of your exact situation. One of these it the problem.
One last thought. The by pass on the softener is not leaking through is it? Check this.
This is just something to add to Jim's answer. PLEASE DO NOT ACCEPT on this as Jim is working this question but I wanted to add this to the possibilities to check. If you have concentrations of manganese in your soil strata and the levels are greater than 0.05 ppm in your water supplies then manganese tends to fall out of solution and form black flakes. These flakes will deposit themselves in the same way iron stains and can clog pipes. Since you are getting this in your well water as well as else where in your system you may want to get a water analysis done to check the make up and mineral content of your water.
Excellent assist. Thank you Patrick.