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If things are still invisible when rendered, then I have a couple ideas.However, I have not done enough texture work myself so I don't have a whole lot of knowledge in this area. Other users more familiar with working with textures will have to confirm/deny my ideas, or you can just try them and see if it works, lol.
Could backface culling being on be a potential cause? Although I don't see why this would affect the result of rendering. It's really easy to toggle on/off though so couldn't hurt to check. This screenshot shows where it is found, its in the 3d view right side panel that is toggled on/off with the "n" key: http://www.html5gamedevs.com/uploads/monthly_10_2014/post-7026-0-10328700-1413142976.jpg
And the blush looks like floating geometry that is being pulled in and out of the model based on whether it is supposed to be visible or not. If it is, and the floating geometry with the alpha shares the "exact" same space as the cheek mesh, could this be a cause? (Try pulling the blush out farther -if it is floating geometry- so there is a gap and see if it still causes that invisibility)
Other than those two ideas, I'd have to assume the issue lies somewhere in the material settings. So you would have to search for stuff relating to setting up transparent materials properly. Don't forget that the rendering engine you use here will matter as well. Cycles material settings work differently than the Blender Render (often just referred to "internal" in the context of render engine discussions) material settings.
3d viewport is on the left, the rendered result is on the right. None of my objects are selected, and Suzanne is visible inside the cube through the transparent parts of the plane. This is just like you are describing your issue.
http://steamcommunity.com/sharedfiles/filedetails/?id=755745804
3d viewport still on the left. Now I've selected the plane. For some reason the plane (while selected) stops making the front part of the cube invisible.
http://steamcommunity.com/sharedfiles/filedetails/?id=755746804
This seems to be completely in the viewport and doesn't affect what is rendered. So you'll have to test what happens when you actually render it. It will probably work just fine if your material is set up correctly.