If you attempt to upload a program using the checksum check option, the flash programmer fails. It all works correctly if the program is uploaded without checksum check as it seems the case with PNut. I don't know what exactly fails because there is absolutely no feedback from the flash loader.
I guess that getptr doesn't return the expected value when the checksum check is requested. The only solution I found is to get rid of it and explicitly set the program size, with this change it works with an without checksum check.