Isboxer not saving macros in addon folder

Yep, you instructed him to remove FTL DPS Keys from the Character Set (Step 4 of your guide) and that's correct, however this does not stop it from being loaded by a Key Map State Action such as the one in Activate Maps (Shift+Alt+M). This only sets the initial state (when loading, or re-loading) of the Key Map to off. Activate Maps in Step 2 sets the state of both FTL DPS Keys and Combat Hotkeys to on, thereby double-binding the 1 Hotkey. Both the 1 Hotkey from "FTL DPS Keys" and the 1 Hotkey from "Combat Hotkeys" will execute, which is why OP will continue to see the 1 pressed in all windows regardless of his Combat Hotkeys, until solved.

I'm just trying to make this clear because it is a common issue I have to help people with in the ISBoxer Chat Room after they have followed your walkthrough, this information is not in your guide.

Crap, I'll have to add that, and my apologies on not outlining it within my guide to all, as well to Lax

[Ualaa]

I usually use a White List for my Keymaps.
Character Sets > The Specific Character Set > Bottom Right Pane -- Second Tab > White List (second option), Check the desired Key Maps.

That way, even if a mapped key attempts to load an undesired Key Map, the character set cannot load something that is not intended for that team.