Try exporting the pictures to a desktop folder, then drag the whole folder to the SD card on your desktop. Sometimes the problem is that they won't go into the root level of the card.
You can rename them during the export from the export dialog to see if that helps. Use Album name would ensure they all have different names, up to 99 photos at a time. For more than 99 photos, group into separate albums, export each album into a desktop folder.