Whenever I'm merging more than two layers into one, InDesign CS6 scrambles the order of content brought in from different layers. This way, Layer 1 being the topmost, Layer 2 next below and Layer 3 being the lowermost, the content of Layer 3 ends up on top of the stack in the final merging result. If I go 2-by-2 layers from the bottom-up, that doesn't happen. Whatever Adobe, WHAT-EVER!
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