As of beta 2, the MG configurator modifies the main glest.ini file, not glestuser.ini. I think this is counter productive, it does more bad than good, since we never ever want glest.ini touched by users, and it just gives the wrong impression that is is okay to edit this file and that doing so will definately result in the changes you made t be applied.
I think the configurator should either be changed to read its initial data from both glestuser.ini and glest.ini, understanding that settings in glestuser.ini take precedence, and then write only to glestuser.ini. Or we should remove the configurator off the release/distribution for now.