While I agree that WEI is NOT a very good bench mark, I see no reason that if you upgrade a GPU - the score would decrease. I would suspect a minor driver issue.
You could run 3DMark06 and compare your results to the norm.
When ever I change a GPU, I alwas delete the drivers, run a driver Cleaner program, and re-install the Cat software suite (even if it is the same version).
I've not had a higher end GPU, memory, GPU give a lower rating than a Lower end counter part. The HDD scores are the only one I've noted discrepencies, ie Mechanical HDD seems to be capped at 5.9/6.0.