It could be that the format of a config section changed, something may be converted to/from an array, settings could move, variable names could change, etc, etc. Lots of different reasons. There is a configuration upgrade process that makes changes to the config as needed. It only happens when necessary.
The config format didn't change from 2.0 through 2.0.3, but it's already changed from 2.1 to 2.1.1.