Regretfully I do not quite understand the term "make up water pH for the BFW" but if you treat your water with an ion exchange bed it will absorb most of the non water ions. Consequently the pH of water treated by ion exchange should be near 7. Due to absorbtion of CO2 which is a weak acid the pH is shifted to 5,6.
It is possible as well that the very low conductivity of water, treated by ion exchange (about 0.5 microS/cm), your pH meter and the electrode chain cannot detect a reproducible signal on the input of the instrument amplifier. Just to check: to increase the conductivity dissolve a minute amount of KCl in your sample- it will not change the pH and make a reading.
There is another possible reason for erroneous readings (-if we assume that you calibrate your pH meter with a buffer solution before measurements and you have removed the protective cover from the electrodes ) and it has to do with the basic pH measurement circuit design: in some cases the imput impedance of the glass electrode pin is really very high, in the order of 10^12ohms, but not of the reference electrode that could be in some designs about few kohms.If this is your case then the reference electrode is not on the same potential as the entire equipment earth or ground potential, which is considered zero.You can check it easily: if your pH meter chain works fine in a completely electricaly isolated glass beaker on a dry desk(plywood, ceramics..but not on stainless steel!)then you have prooved it.You should go step by step and be aware that industrial pH measurement is not very easy because you work in a terrible electro smog surrounding,with a relatively low signal (abot 100 mV)and at extremly high impedance and sometimes with nonconductive liquids.
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