This is a new situation. I have been using the pair together for many years and have never had this problem. Not doing anything new in my work flow than I have in the past. Why now would it show up as RAW? Actualy it does make the change though. If I pull up the original file from the original folder it first must be opened as RAW then once open in Photoshop I check image size and it is cropped. Looks cropped and info size is cropped.
You have a RAW+JPEG pair that you've cropped and then you save as to another folder? PM can't produce RAW files from a Save As. Only TIFF, JPEG, and PSD are supported in Save as. That said, when you do the Save as, you do have the option to apply the crop to the saved image (or not). Unless you're saving to the same folder containing the original images, the destination folder should not have any RAW images in it.
If you're trying to edit the RAW+JPEG pair (the originals, not any saved images) then there is a preference (in the Launching settings) that determines whether the RAW or the JPEG is sent to your editor. If your settings are set to send the JPEG of the RAW+JPEG pair then it is possible that the JPEG is being sent to Photoshop but you've set the ACR plugin to handle JPEGs as well as RAW files and in that case JPEGs will appear in ACR before they can be opened as an image in Photoshop. If the image has a crop set on it, then the crop will appear in ACR.
HTH,
-Kirk
