Comparing it with rsync running on Cygwin is a bit unfair, as Cygwin is known to be terribly inefficient. I don't doubt that their CDC based algorithm is faster, but probably not by the margin they claim if Cygwin is taken out of the equation
hash = (hash << 1) + random_table[data[n]];
bool chunk_boundary = (hash & magic_pattern) == 0;
per byte. That's only a few ops and very cache friendly. The random table only has 256 entries, 8 bytes each, so it easily fits into L1.