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Updated: July 26, 2016
When you do a comparison between two configuration files (running vs startup) that are very large (about 16.000 lines), NPM sometimes does not finish the comparison.
The first config you chose is loaded nearly instantly but as soon as the comparison begins, it does not continue. However, the comparison of smaller config-files (1500-2000) works fine.
NCM version 7.4 and later
This behavior is known in NCM with very large config files.
Use the Config Change report Job when comparing large configs.