You can't avoid it. If you use gradient this happens. That's why I used to remove the top lighting on ARAI 2006 too... It doesn't depend on which program you use, it comes with the tex format.
you can avoid it, you can convert with no loss at all but the filesize goes up quite a lot, thats why i only do it for tyres that are smaller textures,doesnt affect po at all coz its still drawing the same texture,hope this helps