(Copied from my reply to you on the other thread, so that others can find the reply here as well)
You have a older version of the STM32F427 chip (Revision Y). With this version of the silicon, you are unable to reliably access the second 1MB bank of the flash and use the USB at the same time. See more about this error here. Hence if you are using a revision Y silicon chip, you can only use the first 1MB of flash, hence why it your bootloader returns with the flash size being 1032192 bytes instead of 2080768 bytes.
Are you using a normal Pixhawk board?