@jsc I think you should be happy with the recent change. The behavior for the toggling of hidden files is more consistent now. Not sure what my original reason was for doing it the way I was, but you should have no issues now.
So what this means is when a new FuzzyPanel session is opened, it will use the setting in you setting file, then any time during the session you can toggle back and forth and it will remember the state throughout that session (until quick panel session is officially exited/completed). Regex excluded files and hidden are now treated the same.
I will backport this to ST2 later.