Before you blame the Leslie, have you tried clipping headphones to the GG terminals to see if it comes from the organ?
I thought I had this problem earlier in the year but it is just Hammond characteristic crosstalk and rumble. The higher notes are filtered. If you play a 888000000 registration in the middle octaves do you get that sound? I played my clone through the Leslie and got the same effect. If you play along toa music CD you won't notice it.
It took me a preamp, Leslie amp and tone generator recap to realise this [:$]
Also is your tone generator wax capped?