There's quite a bit of difference between the KRACH and the Pairwise, but not until you get down to #7.
I don't know enough about how the KRACH is done to judge, but it's said to be the best out there.
At #7 we have Cornell in the PWR. In the KRACH they are 13.
Duluth is 7 in the KRACH and 17 in the PWR.
Yale is 21 in the KRACH and #9 in the PWR.
I shouldn't complain because our KRACH and PWR are only one off (4 and 5 respectively). While that's a significant difference in seedings it's hard to judge one method more valid than the other.
On the other hand a team like Yale making the tournament says to me that the PWR is fatally flawed.