Its cause you're doing it wrong. In Scrypt mining, hash rates are x1000 times low than SHA-256, so, with a ATI 7970 you can get +- 700 mhs in SHA-256 and only 700 Khs on scrypt algorythms.
You need to read the, Scrypt readme file from CGminer.
Also, in CPU miner you get 3 times your maximun speed, normally you should get 15mhs and 15khs. So i think you may use that 45khs
Sorry for bad english, i'm From Argentina.