I don't mean to bump this thread, only update it for anyone else running into the same problem.
I, again, ran into a sound effect in my game that was clipping at the end of play. I load up XACT and play the sound from there, and it reproduces the clipping. I check out the sound effect in audacity and the end of the sample is zero'd, but not the beginning! So I zero the beginning, load up XACT again (being sure the previous sample is not cached, so I closed everything down and reopened it) and the sample is fixed, no clipping! 🙂
Next, I noticed another sample with a way worse non-zero beginning, and it does not clip.
So, it appears non-zero'd beginnings of some samples cause clipping at the end of play, but this does not apply to all samples.