Thanks for the location. I was thinking that it would create a global config file in the location of the folder, not a single location. I think it might be a good idea to place the global config file in the location of the reprap host software folder, because if people want to try different configurations or testing of the software, they don't want to screw up their "good" settings.
Happened to Ithacacian, his host software was behaving very weird and he redownloaded the host software from SourceForge and it was still having the same issue. If it was stored in the location of the host software, his problem would be resolved when he ran the other one in a new location.