The files on CDs are aligned to 2 kB boundaries. Dedup is looking for n kB continuous block. If the block size of the material you want to dedup does not match to the block size of dedup system, you'll get suboptimal results. The bigger the difference, the worse the results.
Say you have this data:
ABCABCBACCBBABCC
Dedup system that has block size of 1 can see you really have just three unique blocks, A, B and C.Same data, but dedup with block size of 2:
AB CA BC BA CC BB AB CC
Dedup block size of 2 thinks you have 6 unique blocks: AB, CA, BC, BA, CC and BB.Etc.