Are you running any sort of low pass filter? (What filter are you running at the high end?) I agree with others that there may be some high pitched harmonics. If you have a relatively sharp filter at the high end you could produce some aliasing which would sound like noise. This is just a stab in the dark.
EDIT: looking at the pics that skalinder posted, it is obvious there is a very sharp frequency filter at the high end. With the energy right at your cut frequency you will get some aliasing, hence the crackling you hear (but barely, it is hardly noticable to me). You may want to try some sort of filter in post processing with a nice wide taper to cut out the high end.
EDIT AGAIN: Having cleaned 19th century organ pipes and checked out a few old organs in my time, I wonder if there is the possibility that a small leak on a lead to a pipe could cause a high frequency whistle. Do you notice this high frequency energy elsewhere in your recording?