From what I recall and understand, the original ignore tells EVERY ship to ignore that target. Whereas the new one only tells a certain ship to ignore a target.
Yup. Also, the original ignore sets the protect flag on the "ignored" ship. And the comms menu was switched to use the new ignore rather than the old.
Volition really overdesigned that function, with the consequence that you can break a lot of missions in retail FS2. One of the most famous is The Sixth Wonder, where the Colossus simply won't attack the Hawkwood if you told anyone to ignore it earlier in the mission.