I should add that there hasn't been any alteration to the system in the last 2 years - wouldn't any flux residues have been fully dispersed in that time though?
Why? If it hasn't been flushed, where would they go?
Most domestic corrosion inhibitors contain sodium molybdate and are slightly acidic. SFAIK, the advantage of the molybdate is that you can't overdose the system (within reason) and you don't need a test kit. I don't know the theory about how it works as a corrosion inhibitor.
The commonest commercial treatment regime used to be to keep the water alkaline at about 8 or 9 pH and use an oxygen scavenger, such as sodium sulphite at about 50 ppm, to absorb any dissolved oxygen before it corrodes the ferrous components The scavenger concentration needs regular checking with a suitable test kit (£!). The rate of the oxygen scavenger depletion indicates the rate at which oxygen is getting into the system.
Keeping the water alkaline stops galvanic corrosion dead. You could demonstrate that to your self with a bucket of water with a bit of copper tube and a bit of steel pipe immersed and connected through a multi-meter set to measure mA. With tap water there will be little or no potential difference/current.
Making the water acidic (few drops of lemon juice, vinegar, HCl, whatever) will cause an increase in the current. The current is stripping ions from the steel, corroding it. The more acidic the electrolyte, the bigger the current. If you had wanted to generate a current, you'd use the strongest acid you could get (as in car batteries; Breaking Bad reference here).
Active flux contains ammonium hydroxide (I think) that changes to hydrochloric acid on heating; soluble, instant conductive water/electrolyte, instant recipe for bimetallic corrosion.
Making the water slightly alkaline (caustic soda, baking soda, whatever) stops the current.
... wouldn't any flux residues have been fully dispersed in that time though?
PS I just realised what you'd meant by that. The corrosion is not caused by the acidic compounds dissolving the steel, which would deplete the acid. It's caused by the acidic compounds making the water conductive, completing a bi-metallic corrosion cell and allowing galvanic/bi-metallic corrosion to start. That will continue indefinitely.