The filter that is applied to the FDS sound is acting differently across different sampling rates. 96khz doesn't realy filter anything noticeably while 11khz filters too much out.
I already requested that. jsr gave me a no, but that's because he's aiming for hardware accuracy, which is not necessarily bad. However, I did notice the FDS frequency filtering change. I used the tracker at 44.1KHz sample rate before 0.4.2 got released, then I noticed the change in the FDS filtering, and switched to 96KHz, which seems to sound closer to the 0.4.1 FDS, but still sounds different. This would still be a cool feature, but I now realize that NSF players might have trouble with it.