Other effects can prevent a permanent from untapping during an untap step. You do need to look carefully, however, as many effects say that the permanent does not untap during its controller's untap step, and this card's ability occurs during other players' untap steps. If a card does say this, then Seedborn Muse can untap it. But some other abilities are not written this way and can still prevent a card from untapping.
All your permanents untap during each other player's untap step. You have no choice about what untaps.