One thing you should know, the expansion board has organ samples with the rotary on. Actual samples of an organ with leslie applied. On some of the patches, the modulation acts as a crossfade, playing a slow rotary sound with no modulation, and crossfading into the faster rotary sound as modulation is applied. I suggest you turn the effects off completely, so you can get an idea of what's going on. Some of the organs will still have the rotary sound due to the crossfade between waveforms. In this case, there is no way to actually do the speed up and slow down of the rotary, because the effect is coming from the wave itself. My guess is that this is what you're hearing.
You can alleviate this problem somewhat by sending slow modulation messages; move the joystic (or whatever your modulation devise) very gradually. This will make the crossfade slower, giving the illusion of the leslie changing speed, but still not completely authentic.