Are you using 6.31? If so, MED's skin edittor uses an 8-bit palette of which the colors for it are poorly assigned. If you are using 6.4 (caution: public beta), this isn't a problem. To be sure on it, put your test model in WED, build to update entities and preview it that way.
"You level up the fastest and easiest if you do things at your own level and no higher or lower" - useful tip
My 2D game - release on Jun 13th; My tutorials
