Ah yes, sometimes we can guess the answer fairly successfully, without looking at a file. But not this one....at least not me.
But Moini's guess was right on! And it sounds like you might have been on the right track, thinking about layers.
You have a Blend mode applied to the layer (Multiply). When you apply a blend mode to a layer, that also applies a blend filter to all the objects in the layer.
(Technically, I think that's because there's not an SVG standard for layers, so Inkscape creates layers by using special groups. So technically, the blend mode, which is really a filter, is applied to the special group, which we call a layer.)