I would have assumed that the layers would have some sort of keying feature to ensure that they can't be assembled backwards, but if not, then you have lots of combinations to try.
I would check that the colour filter layer is not backwards. That would seem the most obvious to me. If it's backwards, then the colour order goes from RGB to BGR.
If your polarizers are the wrong way around it could cause colours to be reversed. Light is polarized by the first polarizer. The LCD layer rotates the polarization depending on whether the pixel is on or off. The second polarizer filters out the non rotated polarized light (or vice versa). But, if that were the case you'd likely have a completely negative image (light becomes dark, and dark becomes light).