With the update to the haplotype pair ordering function, we break scoring ties on the basis of variant count. With our current scoring model, the hom ref, het, and hom alt haplotype pairs get the same score as long as we have the same number of reads that are a match to the ref and alt haplotypes. I've got a change that I'm hoping to push today that fixes the scoring model, and that will uncomment this line. ;)