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I have faced the same problem. The root cause is that rqt_reconfigure dumps not just the dict containing the parameters, but a Config object where the parameters live.

This happens in the rqt_configure source, file dyn_reconf_client_widget.py:

def save_param(self, filename):
    configuration = self.reconf.get_configuration()
    if configuration is not None:
        with file(filename, 'w') as f:
            yaml.dump(configuration, f)

I don't think there is an easy solution for you, except if you are willing to modify the rqt_configure source code you can find the file dyn_reconf_client_widget.py and modify the second line to:

    configuration = dict(self.reconf.get_configuration())