Nex 7 Raw & Lightroom, odd colours
The result you see in LR is Adobe's interpretation of the RAW file. The "Adobe Standard" profile is usually somewhat different to in-camera jpegs, regardless of the camera brand. There are other, model-specific profiles too in LR - for NEX-6, for example, there is Landscape, Portrait, Standard and Vivid. These are meant to mimic the in-camera processing modes, and they might provide a better starting point if the LR standard profile doesn't seem right.
I haven't really ever found use for the Auto Tone, most of the time LR and I seem to have quite different ideas about how the images should look like. To speed up workflow, it's much better to create import defaults for various situations (like basic NR for ISO3200 files etc.).