I've recommended you to delete the 'main-user.cfg' because it is possible that an error has occurred in this file. This happens sometimes.
If you delete this file, SpaceEngine restores it. From the 'main-def.cfg'. Thats alright.
If the deletion of the 'main-user.cfg' does not solve your problem, then this is not the reason for your problem, and you should leave the 'main-user.cfg' in the future in peace.
I can not say then what is the reason for your problem. I can only recommend SpaceEngine to uninstall and then reinstall.
JackDole's Universe 0.990: http://forum.spaceengine.org/viewtopic.php?f=3&t=546
JackDole's Archive: http://forum.spaceengine.org/viewtopic.php?f=3&t=419
JackDole: Mega structures ... http://old.spaceengine.org/forum/17-3252-1 (Old forum)