I was just testing it on my linux box and it seems to be running sqeaky clean
I do have one suggestion though. To avoid confusion, maybe, you could add an "end of section" tag to the config file. So, for example, you could end each section with [/PLUGINS], [/CVARS], [/TELEPORT_OFF], and [/EX_SCORE_MAPS], instead of a blank line. This is analogous to "bbcode" and "html" style tags.