Can you kindly describe the method you have used to compute the gain by measuring input and output voltages of the opamp?
I believe that PSoC Opamp has low Input impedance of about 1M, which is comparable to your external resistor values, resulting in higher gain than calculated one by standard equation (1+R2/R1). The AMUX impedance should be under 1k, probably unimportant here.
To calculate the gain, I have constructed voltage followers using available opamps and send the output of these followers to output pins. The inputs are tied to the input and output of the main opamp.
That is a very low input resistance. Can you confirm if this is the case?
Have any other users complained of gain issues with opamps? Is there a best practices guide for setting up and using internal opamps?
Take a look at this thread,
For PSoC5LP Opamps are low impedance. PSoC 4 is likely to be similar. Try to use resistor divider of lower values (/10) .