I was using giratina in origin forme and decided to switch to primal form in order to fight regigigas, when I gave it a crystal piece and sent it into battle it was still in origin form, and during the fight with professor maple, and any battle after that. I gave it no item and rather than it being in alternate form it's still in origin form not changing at all.
EDIT: After leaving the game alone for a few hours and launching 1.2.3 from the launcher instead of 1.2.2 from the torrent, giratina is back in Altered Forme. Switches between all 3 forms without issue for now. Could just be that game needs to be redownloaded via launcher and launched from there