I'm sorry, I didn't read your post properly, I thought you had generated the .bin version of the image yourself.
I've replicated the problem using the files you supplied for your own splash screen. I repeated the copy operation to concatenate the files, and that produced exactly the same file that you uploaded.
I then appended your splash screen file to the version 3 7.0 nologo binary, flashed it to a version 3 board, and it worked.
I think I know what is going wrong. The version 2 firmware runs on both 128Kb and 256kb flash memory versions of the ATSAM3S chip. So it uses the last 1K or so of the first 128kb of RAM as nonvolatile storage to save the user settings. This means that if the firmware binary + splash screen exceeds 128kb in length, part of the splash screen gets overwritten by the user settings.
I guess I could fix this in the next firmware release by reading the chip ID register to find the memory size and use that to decide where to store the nonvolatile data.