Make sure the layer transparencies and styles are the same (you can adjust this in the layers window). For example, if you have an underlying layer set to "multiply," it can change the color of the top layer depending on your layer transparency.
You can check to see if the colors are actually different by selecting the dropper tool from your tools window and clicking on you color. The color palette window should open, displaying the color you selected and the number. If both color samples have the same number when you click on them with the dropper, then your eyes are fooling you and both colors are actually the same. If the numbers are different, check your layers.
If you're colorizing your artwork using the "image" menu on the toolbar, check the saturation level. This method of coloring can look different if the two images have different saturation levels. You'll just have to play with it until they match.
Hope that helps.
