Well.... maybe that wasn't it. Cutouts are wrong again. I did two test images before posting here, and thought it was back to normal. I didn't change anything. Now it's off again. I don't know what is causing this.

Edit: Still testing...
At this point the problem seems to be with images created from brushes made by myself or others.
The stock brushes and shapes seem to do ok with cutouts. For example, my butterfly brush won't cut out, but the stock PSP circle brush and PSP heart shape will. Does this make sense? When exporting a brush that I've made did I miss a step? Or is this just coincidence?