I have got a Samsung Galaxy Note with stock rom. I occasionally make Quadrant test to measure the performance of the device. Device came with 2.3.6 rom and I measured 3677 points. After I upgraded to official ICS 4.0.4 I measured 3307 points. Few days ago I got another 4.0.4 upgrade, after that I measured only 3085 points. Thats a huge decrease from the beginning. Is it normal? I always chose the official upgrades, the phone is not rooted. I haven't made factory reset after upgrades.
Quadrant is not a very good benchmark, beacuse the results vary a lot. Try running it four times in a row and you will be surprised. Antutu benchmark is much more reliable.
Don't worry about benchmarks though, they don't tell the whole story on real performance of the device anyway.