It looks like config/config.ini.php gets rewritten on every page request, probably through the call of “forceSave” in Piwik_Config::__destruct.
While the documentation says “At the script shutdown, we save the new configuration file, if the user has set some values” it seems like forceSave does it unconditionally.
Apart from that I suggest that dumpConfig should sort the generated config, to make sure that sections do not jump around in the config file when the same config gets re-saved.