Unless you explicitly bind shift-<keybind>, the default UI keybinds will take precedent. For example, in the default UI shift-1 is the keybind to take you to action bar/page one. If you bind a Macaroon button to 1 and hit shift-1 (to activate a [mod:shift] condition) Blizzard's binding still takes priority. The only way to solve this is to unbind those functions from the default UI. Macaroon has a hands-off approach to the default UI and merely creates virtual override bindings and does not erase anything the default UI has set up.