Stitching Panorama With Rotated Images

I am working on a project requiring numerous panoramic images stitched from aerial photographs shot from a drone. I'm running into a problem where I occasionally need to adjust the rotation on an image in the source and the software is not seeming to honor the rotation when stitching. It seems to take all other adjustments (ex: lens correction). Photoshop stiches them fine, but the "Panini" mode in Capture One is ideal for our use case.