Hi Abhi,
Are you using an NI product? Or just this particular ADC?
If you are using just this ADC, then can you take some better images?
In particular, the X-axis scale on your oscilloscope image is at 5us/division intervals, and it's very hard to see whether the 400ns pulse is flat on the top. That is, it's hard to confirm on your oscilloscope that the pulse isn't discharging.
On your LabVIEW program, the image is also unclear, and I'm not sure what the time intervals (us/div) is on the X scale, or what the voltage intervals (V/div) on the Y scale.
As far as the "discharging" goes, have you compared input impedances (resistance, capacitance) of your oscilloscope with the input impedance of the ADC? Are you using any other sort of probe with your scope or your ADC which has an additional impedance?
I can't think off the top of my head why the input to the oscilloscope would be consistently positive, and why the input to this ADC would alternate positive/negative. Try comparing peak values to see what you find.
-Andrew
National Instruments