How are your devices managed? SSH/Telnet? I find that SSH tends to work much better with NCM.
How do you have it set up to download the configs? SSH/Telnet/SNMP/SCP? Once again, I find it better to use SSH myself.
How are your devices set up for logging in? Just a password/enable, or are you using username/passwords and "aaa new-model". I find username/passwords work the best.
If set up for username/passwords, upon login do you get a ">" prompt and then have to enable? Or do you have it set to go straight to whatever privilege level they have. I find it best to drop them straight to the "#" prompt...