Try adding position = "identity" to your geom_bar call. You'll note from ?geom_bar that the default position is stack which is the behavior you're seeing here.
When I do that, I get:
print(ggplot(melted,aes(x=x,y=value,fill=variable)) +
geom_bar(stat="identity",position = "identity", alpha=.3))
And, as noted below, probably position = "dodge" would be a nicer alternative:
