When playing a low D and a chord with the higher notes for example, I get distortion. Using American Classic Organ disposition. Of course it could be caused by the Realtec AC97 audio driver or even my earphones.
We have to assume that your buffer settings are all appropriate. If you are talking about intermodulation distortion, then it could certainly be due to your earphones, or even your ears!
I have done tests to ascertain the level of harmonic distortion and also intermodulation distortion due either to Fluidsynth or the Realtec drivers, and both seemed to come through with flying colours.