My method for global settings is:
A. Have a setup registration that sets the keyboard the way I want (pedals, assignments, vocal harmony, etc. etc.). For this registration, all groups in Registration Memory are memorized.
B. For every other registration, groups which I want to be global (in my case, Line Out, Live Control, Scale Tune, Foot Pedals and Assignable Buttons) are unchecked when I memorize.
However, Freeze should work just as well. If you don't want Live Control settings to be changed by a registration, then ensure this group is checked in the Menu>Registration Freeze screen. Then ensure the Freeze button is lit.
The downside to using Freeze in this way is:
1. You lose the ability to use Freeze on an ad hoc basis,
2. If you load a registration when Freeze isn't on (eg, you forgot to turn it on after a power up), then your global settings could be overwritten.
So, Eddie, it sounds to me like problem #2 happened to you. You loaded a registration when Freeze wasn't on. My recommendation would be to create a Setup registration (as in A above) which will reset the keyboard to your liking. Of course, you have to ensure Freeze is off when you load this registration.
The advantage of having a Setup registration is you'll always have something to return the keyboard to your preferred settings when something goes wrong.
Cheers,
Fred