AC Master tries to detect if the width and height you enter for a course map are proportional to the width and height of the course image you imported. It does this to check if you've accidentally switched the width and height values. If it detects that situation it will display the message:
"Width/height don't seem to match the image's rotation"
Remember you have to enter the Width and Height for the rotation of the course map image you imported. If you see this message you should confirm the width matches the width of the course map image in the orientation you imported it. In other words, if the course is rectangular and printed in portrait mode on paper but you rotated the paper and took your photo in landscape mode it is likely the width will need to be larger than the height (even though on paper the width is less than the height). The Width and Height must match the width and height of the course image you imported in the orientation of the image.
Depending on the dimensions of your image AC Master might not be able to detect if you've switched the width and height values.
It is also only a warning message and won't keep you from saving your Map.