Seeing your comments on https://www.digi.com/support/forum/64866/full-cloning-one-fully-functional-rcm3100-new-rcm3100-board?show=69323#c69323
Note that extract_flash.c is now a part of the Dynamic C 9 repository on GitHub: https://github.com/digidotcom/DCRabbit_9
I'm not sure what's happening, other than the program incorrectly calculating a program size beyond 1MB. If you can email me a copy of the .bin file, I might be able to figure out why it fails. I do have an RCM3200 that I can do some testing with (and install the binary to by using RFU), but I need to know what compiler version built the original binary. I have not done any testing on firmware build with the Softools compiler.
If DUMP_FLASH works, you could look through the file in a hex editor to truncate the 0xFF bytes from the end. It might even be possible to detect the end in the base64 file and just strip those lines from it.
Maybe uncomment the VERBOSE macro definition and post a copy of the output? And try again with ALTERNATE_PATTERN defined?