These differences can be annoying indeed, as you're experiencing now.
The 3D-preview is a very crudely optimized "render" of the scene, see it as an approximation.
This also means that things aren't calculated as accurately as in the final render, for speed reasons, and results in discrepancies between the preview and final render.
The fact that you haven't experienced it with an other scene is probably because you used different lighting conditions etc. etc.
In general I've never had 1:1 results with the 3D preview. It is very useful for examining POV's and setting up the rough terrain.
For lighting I'd suggest to *always* test it with test-renders, rather than using the preview. It always differs quite some in my experience, especially the saturation of colours (due to lighting).
Cheers,
Martin