Can you link to the url having issues? What version of MooTools are you running? Which browser and version?
I can def hit apply/save so I'm not sure what's going on on your site.
I am really sorry for the issues, I've asked Alex Divine to try an updated version and he confirmed that to be working, finally.
So you can now download the version 1.7.2 from the download page that, hopefully, should work as expected.
Thank you all for your help on sorting out these issues.