Maybe I don't understand the problem you're having, but you said that the color map gets replaced by the transparency map.  I don't see that going on in the material settings you're showing.  If you can make each material zone visible and invisible, can you show some pics of how those materials are set and what the results look like? 

The pics you've shown are only of the previews.  Are you seeing this in the actual render, or are you basing this only on how the preview looks?  Don't trust the preview completely, often it doesn't bear any resemblance to the rendered output.

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