You are probably NOT doing anything wrong. Lightroom auto tone has ALWAYS been a disaster, in fact it used to be worse. Any other program I have tried works better than the Lightroom auto tone. That being said, sometimes it works pretty good and provides a good starting point and you can always just do and undo if the results are bad.
I agree with Bob, but your results seem worse than expected. I shoot with Canon 5D MKII and 600D cameras and Auto Tone results are usually OK with most images, but I rarely use it. Is your monitor calibrated and to what Luiminace level? For most usages a level of 100 to 120 cd/m2 provides the best results.
As others have indicated "Auto" can often be quite far out whilst on others quite close. While I don't have an answer for you in terms of using auto tone with multiple photos at same time I can assure you that Adobe engineers are continually looking at ways to improve the accuracy of the automatic corrections.
Changing the subject very slightly. Are you aware that holding down the Shift key while double clicking on text for Whites or Blacks sliders (i.e. the text not the slider) can often improve the accuracy of black and white point adjustment, and it also limits the calculation for the adjustment to the visible image (i.e. it ignores anything beyond the crop boundary).