Active filter has unintended attenuation for lower frequencies
Your DMM HP3458 setup is incorrect for a low frequency signal.  Perhaps the number of readings is sufficient if using the 100ksps rate in order to capture the entire wave.

Your filter is a bit weird.
R1A * C2A = 50 kHz ok
R1B * C1B = 13 kHz
R2B * C2B =  4 MHz


Update :
The Red Dot is supposed to be null DC as the non-inverting input is reference is 0V this means the DC gain is unity by virtue of R18=R58. So the conclusion is measurement setup error, again.