Differential to single-ended converter
The common-mode rejection ratio (CMRR) is limited by many things. I expect in your case the tolerance of the resistors is the major problem.

To get a rejection of 40dB in common mode the gain from each of the two input signals must be the same within 1%. This requires close tolerance resistors and for dynamic signals even the capacitances need to be matched.

The circuit you are using currently has the same input impedance on each side, the single opamp circuit a different input impedance so any source impedance will cause a common-mode voltage to be present.

The classic differential amplifier actually uses 3 amplifiers and often called an instrumentation amplifier. It has infinite (theoretically) input impedance.


It is possible to get high input impedance with 2 amplifiers with this arrangement:


With all variations, you not only need to be aware of the balance that can affect the CMRR but also the absolute value of the common-mode voltage. If there is too much one of the amplifiers could exceed its capability before the output reaches its limit.