I figured it out hahaha, the autosave was only applying to specific case(inventory updated, quest progressed) so if the player didn't do a manual save (ESC/P to get to the menu) and then exit the game, it would try to set them to (0,0,0) which is slightly under the landscape
I've fixed it (and also initialised the transform in the save file as a backup) but as we can't update it during voting I'll just have to wait until the end of the week
Thanks for your help!