Ok, so it seems the best practice is not to use pngs, but to use psds instead. The reason I didn't do so is that I was worried about file size (my psds are nearly five times the sixe of my pngs), but apparently the file gets compressed anyways so it doesn't matter.
To fix the issue I just saved it as a psd and not a png and left all of the rest of the settings the same.
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