Auto Rotate problems when shooting tethered overhead

I am shooting with a Canon 5d mark 2.  When I shoot product into the auto rotate works properly and the image appears rotated properly. Although when I shoot overhead or down on product it seems to get confused. If I rotate the camera twords the horizon and fire it figures out which way it should be the I can reframe my overhead shot.  But if the camera is moved at all it will show up rotated the wrong way and I have to slightly move the camera away from its directly overhead framing again so it can figure out wich way it should be rotating. I have tried all three rotate modes with the camera with similar inconsitant results. What is the best setting on the camera to get consistant results. Or ii I turn auto rotate off is there a way to tell lightrroom to rotate it properly on import like it does for all other settings like white balance.

This isn't a function of tethering, I wouldn't think. Many cameras have a sensor that determines the orientation of images so auto-rotate works. The problem is that these sensors generally only work along one axis, using the force of gravity to tell them where down is. When you orient the camera such that the lens is pointing down most sensors no longer are able to determine whether you are in portrait or landscape, because there is no down -- it ends up being somewhat random.
I've seen this on many different cameras, and all without tethering. It has to do when the sensor is read when composing the short.
Your best bet is to set the camera to ignore the sensor when taking pics like this, and rotate the image by hand that are need to be in portrait. If there is no rotation in the image metadata, Lr will not rotate it. It will have to be done by hand. It won't be that hard to select a number of images and bulk rotate them.

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