If you work on raw files, RT doesn't modify the file itself, it only shows the area which will be cropped. When you reopen the file, the crop area will be displayed again because the raw file is not modified. When you export to jpg or TIFF or PNG, the output file will be cropped. The advantage of this is that you would always be able to adjust the crop area by simply dragging the borders. I think most raw converter act this way, at least it's not something never seen before.