Well, I can permanently remove that line, but the intent is to keep your ISBoxer Jamba settings separate from your non-ISBoxer Jamba settings, because ISBoxer modifies them.

If you do not have a Jamba.lua, but do have a Jamba-ISBoxer.lua, the settings get reset each time. It doesn't reset for me, but apparently for some people the game renames Jamba.lua to Jamba.lua.bak at launch time.

Edit: Future ISBoxer downloads have the line removed.