PH Water Measurement

We have a problem in PH Measurement with PH Transmitter from Yokogawa (Flexa). The problem is, we already calibrate the PH Tx with 4,7,10 PH Buffer, and then we've compared to the PH Meter Portable, when measuring the Buffer (4,7,10) the PH Tx and Portable PH Meter shown a same number, but when we comparing to the Actual Water in Proccess, there's a deviation +- 1,5 between the PH Meter Portable and PH Tx.
Anyone in here have any advise?
What is the process water? High purity water can cause issues if the pH probe isn't designed to handle low conductivity water. High purity water is also susceptible to atmospheric CO2 intrusion which will lower a grab sample pH versus an in-process measurement.

Are the process vs. grab sample temps the same, hotter temps will typically lower the pH reading.

Yokogawa's also have a "process temperature compensation" option which alters the measured pH to correspond to what it would measure if the sample was 25C - is this enabled?
Electrical currents flowing through the medium can apply a voltage at the pH probe and affect the pH reading (which is a voltage reading). A battery powered portable might well have an isolation factor that an AC powered bench or process meter does not.