I am seeing a few differences between amplitudes of scope shots and AI acquistions. The scope has an input impedance of 1 M ohm. What is the input impedance of the PXI-6225? The manual does not seem to indicate this.
Specs claim that the 6225 has 1 Gohm resistance with a 100 pF capacitance.
Maybe it is the difference in capacitance between the two instruments that is creating the differences. A scope usually only has a few picofarads capacitance.