It sounds like you're running into a known bug with Photoshop CC where if you have multiple subpaths on a single layer (or path), only the selected ones will be affected when you crop, resize, or rotate the image.
The workaround for now is to make sure you select all the paths in the image before you resize, crop, or rotate. The easiest way to do this is to drag over the entire image with the Path Selection tool. (Note that if you have any paths not attached to layers, you'll need to select all of them in the Paths panel before dragging with the selection tool.)
Let me know if this isn't the same issue you're seeing.
Thanks Jeanne. This is indeed the issue and the workaround seems to work.