Sorry about the late reply. These were the settings I used. Same?
I'll also throw in the C# program that I used to compare the dump to the rigol firmware image and to extract sections of it as a .hex file for writing. I have not cleaned it up, so there are hard coded paths and firmware offsets, but perhaps it can be useful.
Edit: I had some trouble dumping the flash sometimes, probably because of the state the hardware was in at the time that topflash started accessing it. I found that it was safest to always start by dumping the first 32 or so bytes from the flash before doing anything else, just to ensure that nothing else in the scope was using the data bus or address bus, and if those bytes came out wrong, I restarted before trying again.