When the script is checking to make sure that the file is an image the only thing it is checking is the file extension. So if the file extension is already jpg then there is not anything that can be updated in the script to allow it to work with the files. If we could determine that something in the script was not working correctly then we may have something we can update but at this point that does not seem to be the case, especially since it does work correctly in IE. If the script was treating the file differently because of the format used it would do so in all browsers.
As for the end result of the file after you upload it what happens when you attempt to open the image? If it is an image file it should do whatever default action it would normally do when you open an image.