Figured I'd put in an update. The above issue was caused by not doing a /console reloadui after changing the /assist macro to use ], so it was using the old macro, which happened to be /targetexact.
What that did prove was that ISboxer is sending the keystroke, the macro is executing, and FTL is working (Follow FTL is also working too).

After going through just about everything imaginable, this is a weird issue. The only command that is not working is /assist, and it is not because something else is picking up BACKSPACE, because it was changed to ], and after reloading the Addon, still no Assist.

All addons disabled, cache deleted, attempted using to invoke the macro directly (with the appropriate modifiers and keycombo).
Short of attempting typing out /assist CHARNAME on the console, or even creating his own macro with the same damn thing, and seeing if that would work, I got a bit stumped. It's almost like the /assist alias is being ignored or overwritten. This might be corruption, which is pretty much the last thing I can think of that would cause this; it's just that it is so damn specific.