Just moving a string in a magnetic field, or stressing a piezo can generate a low frequency signal.
My SWR amp does this in a HUGE way as compared to other brands. This is based on very similar tone settings when played normaly. Could be that they have a built in low frequency bump in their design that others don't, or, perhaps the other brands don't have as flat a response curve.
Have very limited experience with separate pre / power amp rigs design to towards audiophile specs so perhaps the issue occurs with separates as well.