I have been having a problem with my image shifted to the left, and wrapped around to the right. This has been reported several times in this thread, however I have not seen this issue directly addressed.
After messing around with it for a couple of days I have found a soulution.
The image I am working with has only 9 colors. If there are not exactly 16 colors in the color table, bootskin will get confused.
In Photoshop (my version at least), if an image has less than 16 colors, and Palette is set to an Exact, or Local palette, and Colors is set to 16, the number of colors in the Color Table will be set to the number of colors in the image, not to 16.
The workaround is to pad the color table with additional colors such that it contains 16 unique colors. If the colors are not unique, Photoshop will remove the duplicate colors when saving the file.