I can't replicate the "to be" example neither. I write the "to be" quote horizonally in row 5, 3, 2, 6, 4, and then I take out the letters from column 5, 3, 2, 6, 4, 1. My coded text comes out as
T O O O Q H T T B H T O S O T
I B N R U A T I E E E N E T S
By the way, if there happens to be a row of blanks in the middle of the horizonal fill-in operation (as a result of say this scrambling vector ( 1,2, 6, 3, 4, 5) ), how would that come out in the encoded text?