My Fragment Shader takes in a nxn texture and a nx1 texture.
These two are multiplied together,
but when i do multiply them together, then it doesnt take the exact coordinates (as my results arent the same through the fragment shader as through doing the calculation on the CPU)
I do not understand how you want to multiply the nxn texture by the nx1 one. Can you elaborate a bit more what you are trying to do? The fragment shader code would be helpful too.
How do you calculate the texture coordinates and what filtering mode is set on those textures? It is possible that you sample different texels or even combination of them (if filtering is enabled).