It seems that when the height of the tracker image is bigger than the width, the XML that gets downloaded from the Tracker Manager uses the "width" value as the height value.
Eg.: if i upload this image (http://www.farmvertical.com/wp-content/uploads/2007/10/vertical_farm_v2.jpg) and set the width to 200, then download the targets and check the XML file, it will look like this: <ImageTarget size="150 200" name="building"/>
It seems that the value of "width" that the user enters is used for the longest side of the image. This then causes problems with the measurment and positioning.
Note: I didn't try with this specific image, but tried with few others (which I can't give ot publicly) and the problem persists.