Trinath,
1-What is the quantity structure date you are imputing or defaulting when you are running CK11n/Ck40n?
For example if your Valid from date has 27/08/2013 to 31/03/2013 and quantity structure date is 01/08/2013 then it will not work. make sure the quantity structure date is 27/08/2013 or later.
Another way is make validity date from 01/08/2013 to 31.03.9999 then run ck11n or ck40n.
Best regards
Hrusikesh