I'm so glad you asked! This was a pain in my side at a particular customer.
The first step would be to follow this KB:
http://www.symantec.com/docs/HOWTO10091
Set PreferredNSHost in the registry to the FQDN/SSL name of the server, restart services, and run a package refresh.
If that's not successful, check out this KB:
http://www.symantec.com/docs/TECH171971
Regarding the "in isolated cases" in TECH171971, I'm the "isolated case." So if all else fails, run TRUNCATE TABLE SWDPackageCodebase as specified, then run the refresh to repopulate it.
Does this help?