Magents from layers that are hidden still affect other magnets. You would expect that if you hide a given layer with a magnet tag, it would no longer have an affect on other magnet-tagged layers/handles, but they do.
As a workaround, I've had to clone the puppet and turn off the magnets on the hidden layers, which is less than ideal.
Have you tried using triggers and swap sets to "hide" the layer with the magnet? If just using the eye icon or opacity setting I could understand magnets are still working. If its in a trigger (so not appearing until you press trigger) then I am more surprised.
I have tried both plain triggers and swap sets. I've messed with it for hours. I'm pretty sure it's a bug.