Sounds like you have something in the pre-amp that is vibrating and this vibration becomes amplified by the shelf when you sit it down on the shelf. Next time you place it down put your hands on the shelf and see if you can feel anything, either on the shelf or on the amp, and notice if when you place you hands on these if the sound of the hum is attenuated. If you can feel a vibration, try putting some isolation devices between the pre-amp and shelf. If you can't feel anything, try covering the top of the shelf (and under the pre-amp) and see if this helps deaden an air transmitted vibration from the pre-amp. FWIW I have an amp tranformer which hums and the hum is very audible in open air and even worse in an enclosure, but when I deaden the walls inside the enclosure the humm is minimized because it is not reflecting off any nearby surfaces.
FWIW, just a WAG.