Reference point losing it's position when Batching

Earlier, when I was working with Batch, I was able to select a reference point and anchor it in the desired position for every photo. For example, when transforming portraits, before starting the batch process, I would navigate to my actions, double-click on "Transform layer," select my reference point, and position it on the subject's eye. This allowed me to consistently transform from that specific point. However, now, even if I place the reference point where I want it to be, when I process with batch, the reference point ends up in a completely random location, often in the upper left corner of the photo or within the Photoshop application itself.

Please help. Is it some hidden option? It's happened overnight, I do not remeber changing any settings (but it's still an option :v)