I have had some trouble getting the one instance to work, My attempts are commented out in the main method of the source code.
I was able to get it to work, some times and some times not, etc. Its currently not reliable enough to be released in the code. Can't have people locked out of the application
Changelog
Your problem with the game modes is most likely not related to McLauncher. The only thing McLauncher directly effects is the mod-list.json, and launching factorio with no args. Now unless something changed with mod-list.json that im not aware of, I don't know if that is related to Mclauncher.
V0.4.6 release and download.