When loading an image with a rotated geometry (e.g. brain.nrrd), the Image Cropper plugin shows a warning about the pixel alignment which can be fixed by doing a reinit. After the reinit, the warning message still remains, though. It should vanish, as is also the behavior when performing a reinit before opening the plugin. In that case, the warning doesn't show up.
After looking into the code, it seems to me that the warning is just formulated wrongly. A simple reinit will not make the bounding box for a rotated image pixel-aligned. Implementing this would take some time and require a lot of reworking the bounding shape interaction. As this is not currently requested, we will keep things as they are and only update the warning text so it won't be misleading.