Common problem with these systems. You have to top the fluid up really high in order to get it into both chambers. While one may look normal, the other one can run dry. They are seperated for a reason. The mud is water saturated fluid mixed with contaminants such as rust and corrosion.

I rebuilt my front calipers after they had been neglected for years by previous owner. No amount of bleeding would have flushed the jelly I found in the bottoms of the caliper bores after removing the pistons.