Chandu,
1.Is there a singe tone sine generator that you can use to test this with? I can't see how you would not get a filtered signal on the output of the AFE.
2.What is the resonant frequency of your transducer?
3.How did you capture the input signal and then compute in Matlab?
4.Can you change the LPF Settings to higher and see if there is a difference?
Thanks,
Chuck Smyth