After I unchecked the flip option, the textures converted but they were not mapped correctly in KSP. So I guess the next test will be to flip them before converting and see if they still load correctly in the game.
Yup, that did it. I flipped the png vertically in photoshop and then ran it through the converter with flip unchecked and it loaded correctly in the game. Probably too much work to do it that way though.