CudaMiner 1st version GTX 295 75 khash/sec
CudaMiner 10/04 GTX 295 56 khash/sec

I concur, this is a step backwards. But on my GTX 260 I do not see the same regression. In fact the card is the same generation as yours. Strange.
I don't think my gtx260 saw a change either. My fermi cards did though...a very nice change in fact. ~30kh/s change.