Your initial post didn't seem to indicate to me that this happened in Firefox too; as it's written, it just says you used to use Firefox. Ok, less obscure now.
As to what it says in the FAQ, non-American users will get this message for Google, yes, but this shouldn't affect whether or not the "Don't show this again" checkbox is saved and remembered. That should work the same for everyone. I can test show this by simply going to one of the international Google domains manually, and it seems to remember it fine for me (yes, Flagfox 5.2.3 is the current latest release). The error message you posted looks like it's probably unrelated to anything here (95% sure-ish).
Could you please check what Flagfox has saved to disk for me? Open a file explorer and find your Waterfox profile, which I would assume is somewhere nearby to where
Firefox's profile gets stored. Then find the "browser-extension-data" folder in your profile. This is where Mozilla profiles store WebExtension storage data for addons, by addon ID. Flagfox is 10 years old, so I've got a lovely old-style GUID: "{1018e4d6-728f-4b20-ad56-37578a4de76b}" (usually the only one that starts with 101). In that you should find exactly one file: "storage.js". Open it in notepad and please paste its contents here so I can examine exactly what's getting saved to disk for Flagfox. You'll want the following in there somewhere (should be near the end; it will need to be inside the normal "{}", so I wouldn't advise mucking with it unless you know what JSON is):
If that's in there, then it's saving properly, but not reading correctly on startup, or something. If it's not in there, then it's not saving properly.
I may as well just give you the sledgehammer fix, as I don't want to take up too much of our time with this. You can revert Flagfox 5.2 to use the old Firefox pref system instead of this new-fangled WebExtension crap by going to about:config in a new tab, then right-click somewhere inside the list, and create a new boolean value named "extensions.flagfox.FORCE_OLD_PREF_SYS" and set its value to true. This'll turn on a debug feature I left in and revert Flagfox to the old system; you'll be able to type "flagfox' into the about:config search bar and all the stuff should show in there, complete with default values. If you do end up doing that, and it still doesn't remember the setting, then you've got something set that's preventing Firefox/Waterfox from properly saving settings at all, which is a far more serious problem. Do note that whilst this prefs backend reversion is reversible by just toggling that new pref back to false, if you don't do that with Flagfox 5.2.x installed then you'll lose your Flagfox settings for Flagfox 6.0, because Mozilla provides no migration for the old prefs system in Firefox 57, whatsoever (which is dumb as hell, but the least of their sins).