Glad to hear that it works outside the tool's root folder, at least you can use it while it gets fixed. :)
This is the same thing that happened to me. I was trying to save in a Desktop folder.
I think this is more of the limitations with GameMaker. I recommend using INIs or checking if save was successful (it should return a flag). If it fails, show an alert message that tells users where they should save.
Also, not sure if you do this already, but consider saving the directory they last used in an INI and always default to that directory.