Custom properties allows property names with spaces. This allows GroupTool to create a file with XML elements with spaces, causing parsing errors. Either spaces should be allowed in property names or spaces need to be converted for XML files.
Ran into this problem while creating my own game settings file and then adding some groups. I saved the Group Set, closed InitTool and then opened it up again. InitTool would not load - it got hung up on parsing the XML, thinking the elements had attributes.