Solution
PXIe-4309 has an anti aliasing input low pass filter on each channel which prevents the high frequency undesired components to be sampled by the ADC. This filter has a gradual roll-off starting from 100 KHz to 1 MHz as depicted by the below Magnitude Response plot in PXIe-4309 specifications.
Hence, the drop in measured voltage beyond 100 KHz is the result of decrease in gain of the anti aliasing input filter. Also, the cutoff frequency of this filter is not user configurable and does not change with sample rate.