Solution
The fluctuation is cause by the incoming signal that have a high fluctuation at a higher frequency portion.
By default, the NI9253's Filter Frequency setting follow the Data Rate setting. For example, when Data Rate is set to 2.000 kS/s the frequency above 2 kHz is cut off by NI 9253 built in filter.
On the other hand, when the Data Rate is set at 1.000 kS/s, the Filter Frequency is set at 1 kHz which will filtered out the fluctuated 1 kHz and above portion of the signal.
In order to get the same result as Data Rate 1 kS/s when running at Data Rate 2kS/s, you can change the Filter Frequency setting to Data Rate / 2 (1.000 kHz) as shown below.
