The download_flash.c sample downloads a complete image of the serial flash, and you just want the portion at the start with the firmware image.
If you look at the file with a hex editor, you'll see a firmware_info_t structure somewhere in the first 1KB of the file, on a 64-byte boundary. Look for the sequence 'BUD!' which is the signature of the structure. You can look in board_update.lib for a description of the fields. With that information, you should be able to identify the length, including CRC, at an offset of 7.
Try truncating a copy of the .bin file to that length and see if it will work with RFU. Also note that there's a GUI version in the Utilities folder called RFU.EXE.
If you're using the "power-fail safe" option of the Remote Program Update feature, it gets a bit trickier. There will be a fake firmware_info_t in the first 1KB, a firmware_info_t for "image A" in the next 1KB, and then another firmware_info_t later in the flash representing "image B".
If this doesn't make sense, just email me the .bin (add a dot to my name, at digi.com) and I'll extract the image(s).