Although I didn't take the actual paper test, I've always thought I would have done better on the paper version versus the computerized version. For reading comprehension especially, I like to underline and make notes, which helped me improve my score when I took paper-based practice tests. For math, it's annoying to have to look down from the computer screen to look at your scratch paper and transfer the information, etc. There's always the risk of miscopying something, too.
I don't think my score was that drastically effected, but I would prefer to have taken the paper-based, if it had been an option for me. I think it most likely depends on how you are as a test-taker in the end, though.