Solution
The main difference in an RTD Acquisition Module is that it has a Current Source which is used for the Excitation. The current source will make sure that current flowing in the RTD is the same irrespective of the lead resistance. As opposed to using the Multifunctional I/O which in most cases have Voltage Sources which will have some voltage drop across the lead resistance and therefore less accurate measurement of the RTD.
To be able to get better accuracy you need a method of inferring the current flowing in the RTD which can be done by adding an extra resistor as shown in the circuit below:
Since you are using a Multifunctional Card you can use an AO Channel to output voltage signal for the RTD. Then Using an AI channel or a Voltmeter shown as XMM1 you can get the voltage VM which is the voltage across RK (Resistor of known value). The current in both the RTD and RK will be VM/ RK.
The resistance of the RTD can then be calculated as (VO-VM)/(VM/ RK).