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.