You are misunderstanding how the arguments to boxplot are used. boxplot(values, ) does not actually move the box plot to the x-value of 500, rather it just labels the box plot with an x-value of 500. The box plot itself still resides at x=1.
To accomplish what you are trying to do, replace the line with
boxplot(values, Y, 'positions', Y);
The 'positions' argument designates where the box plot will actually be placed on the graph.