When configs from a WLC device are used for comparison, you see several flags for changes of lines that have a variable output. For example, system uptime.
All NCM versions
If you are using ssh or telent set to transfer the configs, the default command is show run-config. This is a very verbose output of everything that is happening on the config. This output is likely to change from one moment to the next and is not recommended.
Even with using the best method of TFTP (as this is an actual config file), there will always be a change. That is the file name of the file being transferred. This is because NCM has to name the file to transfer and it will be a random file name each time.
Change the protocol for transfer configs using, to TFTP.
Click here for instructions and example of creating a comparison criteria