Everytime I have to power down the console and IO, I lose all my custom buttons on the console and all the IO settings.  In other words, the buttons on the console that short-cut to Staff View, Next Marker, Event List, etc. get blown away and all my mic pre settings are gone.  Is there no way to save this?

Have you tryed saving it in the project file you created those settings in? By saving the project after making the changes? Also, have you tryed saving them as part of a screen set? There is also the ability to save them as an ACT setup, for the console buttons.
So, you'd want to create the ACT setup, save it. Save the project. Create the Mic Pre setup, save it in the mic pre section. Save the project again. And so on for changes made.