If a domain is registered with GoDaddy.com, sometimes you might have problems setting your custom nameservers viz. ns1.yourdomain.com and ns2.yourdomain.com. Inorder to do so, go through the following steps:
Logon to
GoDaddy.com control panel
Select the domain for use with the name server
Click the [+] next to Domain Host Summary
Click "Click here to see details or to modify"
Enter each host as applicable, then click Save Changes.
Your custom nameservers are registered now, and they should propogate in 24-28 hours.