It is most likely acid rain spots which are hard to get off. But it could be from getting wet and the wax drying differently. Try to buff it out, if that doesn't work, I will try to find out what will.
'95 Contour GL, zetec mtx, drop in K&N, exhaust res removed, 4 10" Kenwoods powered by 1000W Visonik amp, 4 5"x7"/6"x8" Visoniks