Presumably you are using the included St Anne's sampleset?
If so, then there are two ways I can think of where you could have a lot of stops selected without any being visually drawn on the stop jams. (I am assuming that you can hear organ sounds, just not changing ones?)
The right hand pedal is a crescendo pedal which if depressed will add stops. So make sure that is up (I think).
Also, St Anne's has some buttons marked something like FF, F, P etc that can also select stops without you noticing. I am guessing that you have inadvertently selected one of these options and that that stop selection is masking the one you think you are making with the draw knobs.
It should all work in the fre version as far as I know.
If you still have a problem come back with some more information and I am sure someone will help you out.
Regards,