Ys Book I & II ( http://redump.org/disc/32091/ ) states that "The first 2 sectors of the 3rd track's pregap are scrambled data sectors."
This is actually wrong, it should be the first 3 sectors, not 2. I was fixing a clone CD version of this from the Trurip set to match the new database entry here at Redump when I discovered this. The trurip image was perfect except the checksums for track 3 wouldn't match until I scrambled the first 3 sectors of it instead of just the first 2. I managed to figure this out comparing the USA version to the Japanese version with a hex editor, the japanese track 3 is correct but is also 1 sector smaller in the pregap than the USA version. I thought I should bring this to your attention so no one else pulls their hair out trying to get that track right.
So there's 3 scrambled sectors, then zeroes, and then the actual non-zero data starts at offset 376240 (5BDB0).