That's because of the different lengths of $6 (1 or 2) resulting in a different FS count after it, so sometimes "ALA" shows up in $8, sometimes in $9, and the fields to follow as well.
As Scrutinizer posted, modifying the field separator is responsible, as it changes field numbering. $6 now assumes the values "C", "N", "O", "CA", "CB", whose count is 5.