The fix I found for this (with Python under Windows 64bit) was to go all the way to the folder that has the OpenNI dll, where there will be a configuration file called Orbbec.ini. Assuming you’ve downloaded the OpenNI SDK from the Orbbec website, then it would be under OpenNI_2.3.0.55\Windows\Astra OpenNI2 Development Instruction(x64)_V1.3\OpenNI2\OpenNI-Windows-x64-2.3.0.55\Redist\OpenNI2\Drivers.
In the configuration file, there is a line that is commented, something like
;Registration=0
Uncommenting by removing the semicolon and changing Registration to 1 fixed it for me. However, there will still be quite a bit of padding mind you, but pixel (x,y) in the RGB image will correspond to the same (x,y) pixel in the depth image.
If this doesn’t fully fix it, you may also have to change the Resolution setting (make sure you go to the one corresponding to the depth stream), since the depth stream resolution is not 640x480 but 640x400 (or 1280x800). The number corresponding to these non-standard resolutions is unfortunately not shown in the comments, but I found somewhere online (can’t remember where) that 17 corresponds to 640x400.
Hope this helps!