Coolant flush

You should have let it happen in the first place. Once that happens it forms a red clay that builds in layers. Every time you flush it, you only get the outside layer so the flush looks clear until it runs a while and then more of the red clay mixes in again. Try running some strong flush chemical in the system before flushing. I have even seen some people use a little muriatic acid for flush but you have to be very careful and flush it all back out completely. It may flush a little more thoroughly if you remove the thermostat during the process and put it back in later too. This condition develops when you add water instead of coolant in the system. You can't do that, even for a little while.