I was wondering how important the Encoding was for the mms.cfg configution file. The Admin Guide recommends UTF-8 or UTF-16. It has also been stated that the mms.cfg can be over-written and set to the default settings when Flash Player is uninstalled. I have noticed that when this happens and there is an uninstall of a non MSI installed version of Flash Player (EXE) the mms.cfg file is found re-written in the ANSI encoding format and not UTF-8.
I do not know why it is recommended/required to save the mms.cfg file in Unicode format; all the data are purely ASCII characters.
So if you observed that the file is saved as ANSI by the MSI installer, and that the setting work, then I wouldn't worry about it.
But it would be interesting to hear a comment from the Flash Player team.