Can't figure out how to get around this problem using layers and layer styles in CS4, and it is easily replicated using the following steps:
1: Start with a simple image, even a triangle on a plain background.
2: Select the object (triangle, in this case) and copy/paste it onto its own layer.
3: Reselect it, add a bold drop shadow.
4: Add an giant inner bevel (using Chisel Hard, and depth and size sliders almost all the way to the right.
5: Add Texture, with Scale =440 and Depth = -2.
4: Watch the texture while you flatten the layers. The texture changes in size and depth, and the brightness and saturation also change, as well as the direction of the light, even though I left the Global settings on the light.
I had done this with another couple of techniques to produce some very striking effects, but flattening the images always reduced what I was aiming for. I've been using Photoshop for many years and never experienced quite this problem. I tryed changing all of the options within the Layer Styles tabs, but nothing seemed to address this issue.
How are you flattening the layers. Quite often you can different results by using merge layers, merge visible or flatten image.