Dump32 creates a shorter dump that can't be compared with dump made by hardware (512 bytes per sector, 32768 sectors).
Go back to the guide, there is a reference to tmbinc's software dumper. Follow the link, get the source, replace 2 with 3 in the source, then get the dump you can compare with the one you obtained from hardware way (512+16 bytes per sector). If you get statuses with command 3, they are bad sectors report. Write them down, that can help to understand malfunctions of tools. Command 2 won't dump bad sectors if they exist, so that's why its dump is not good for reflashing or comparing. Command 2 can issue statuses, that are reports of unused/blank sectors (ofter located at end of Nand).
I don't think you can obtain a bad 1bl.bin file...
If dump made with command 3 matches hardware dump and cpu key is good then recheck if you understood what the 1bl.key is.