Hi Ronnel,
I had a similar problem, where my manual download was working fine but the job was not working.
I tried the following and it worked for me:
Go to NCM Setting -> Config -> SNMP config Transfer timeout and changed it to maximum value of 14 min. And it worked fine.
The only explanation I have for this is that NCM takes time to identify the contents for the Config.Through manual download, we are downloading only the either the Startup config or the Running config at a time, but my Job was scheduled to download both the Startup and Running config. So the number of downloads for the job is just doubled, which requires suffice Transfer timeout time.
Let us know if this works for you, or the troubleshooting you did to resolve the issue.
It would help others.
Good Luck !!!