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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.
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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.
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I have tried both plain triggers and swap sets. I've messed with it for hours. I'm pretty sure it's a bug.