I've experienced this too. I couldn't figure it out but since I usually pick my own colors to stitch out designs it didn't bother me too much.
Someone mentioned Sew Iconz. I am using the trial version of it this week and, although I love it, it changed the colors on several of my saved designs. I thought that was odd too. I have a design of a pure white dog (alaskan eskie) and Sew Iconz changed it to a blue dog in the thumbnail view...lol