Generally I have found that most Sony CD-Rs are quite poor quality (see my review: Sony 48x CD-R Review
The reason one drive performs better then the other is probably due to one drive having better error correction abilities then the other. Your Samsung Combo drive probably has a much higher C2 error tolerance then the BenQ DVD burner does.
The reason you can view the .avi's better then copy them is because when you are copying the files, you computer wants an exact replica of the original file, and will fail to copy if there is an unrecoverable error. When you play a movie, it has error coverup abilities (like when you play a scratched audio CD and you hear pops and clicks). This is what is happening when you see the pixilation. Using software like badcopypro might allow you to recover your files a little better, but it sounds like you've already done a pretty good job on that.
I hope that clears things up a little for you