What does it mean for an amino acid to match with itself 99% of the time in a PAM1 matrix?
It means that the 99% of conservation of amino acids is just a mean value for all the amino acids. That there can be amino acids that are less conserved and some that are more conserved. 

So from the 21 basic amino acids, arginine is more conserved than lysine in those alignments. But in general they are conserved the 99% of times.