Many glass bowls have the inner layer of glass impregnated (don't remember if it is actually impregnated or vapored on) with either silver or gold. As you use the pipe, some of the smoke will adhere to the inside of the pipe and will begin to change color.

Silver = blue
Gold = yellow / gold

When you clean the bowl with something that removes the buildup, the color will disappear and will start building up again as you use the pipe.

Hope that helps,

Grow