Best I can guess, this plugin looks at the EXIF data, not the actual image dimensions of the file on the server. Maybe it's something else, but here's one issue I noticed on all/most of my images:
Details of the actual image file (never processed by Imsanity plugin): http://regex.info/exif.cgi?dummy=on&imgurl=http%3A%2F%2Ftourkick.com%2Fwp-content%2Fuploads%2F2012%2F12%2Fkitchen-IMG_5804.jpg
The file in the Media Library: http://cl.ly/image/0m3x0F3Z2X3x
My settings: http://cl.ly/image/3U3c0g0f2f2y
The file detected as too large in size: http://cl.ly/image/341Z210Z2D1X
-file is already 1333x2000 but EXIF image size says 5184×3456
-this plugin detects it as 5184×3456 even though it's truly only 1333x2000 on the server
Hope these details help figure out what's wrong. Thank you.