The github version adds maybe 10 or 15 kHash/s more (by supporting the -C 1 flag). It will be in the next cudaminer release, toggether with scrypt-jane (Yacoin) mining support.
git pull and build the latest (with all the latest scrypt-jane h4x), I get 10khash/s less than if I git reset --hard 744d7b7923e106fadfc20eff9833d5d7a5da93c8 (December 28th) on scrypt, on my 660ti.
Does anyone else see this?