I have to say, I'm a bit surprised Train of Thought is seeded as high as No. 4. Probably explains why it's getting utterly tonked by the lower-seeded SFAM.
SFAM lost rankings because it was dragged down by Regression and Through My Words (and One Last Time being relatively short doesn't help either). Train of Thought has only 7 songs and better chances of having tighter results. Quality of the album aside, it's no wonder that Six Degrees with just six songs managed to be the top #1 album.
Yup. As per the original post in this thread, the seedings were "Based on % of Songs placed in the Championship Tournament." TOT had 5/7 songs make it (I assume Honor Thy Father and Vacant were the two that didn't make it), so its percentage was .714. SFAM got 2/3 of its songs int he championship bracket (not sure what the fourth song was that didn't make it), so it had a lower percentage (.667).
Note that SDOIT benefited from this method of ranking (and from having all of disc 2 being considered a single song), but one of its songs got unceremoniously bounced in the first round (and, IMO, didn't belong there in the first place).