On 16:9 shows like appjudgment or hdnation, they sometimes play clips that are cropped within the full 16:9 size. If mplayer-wrapper.pl happens to sample those clips instead of the main show, it will think it should crop to fit the clip.
The primary motivation for this was to compensate for old 4:3 video that contains a 16:9 aspect ratio video with horizontal and vertical bars. I propose fixing the algorithm to focus on 4:3 aspect ratio videos and ignore other aspect ratios.