Which version are you using? Can you give a brief demonstration of the problem?
I do not find the problem to occur in the following example:
z = rand(64,64); X = sort(rand(1,64)); Y = rand(1,64);
pcolor(X,Y,z); hold on; stem(X,Y)
The stem plot is not very readable in this case, but it -is- on top
of the pcolor() plot, and no extra white background is introduced.
Based on your description it almost sounds as if you forgot the