We're using the i.MX53 on a Karo TX53 board.
I managed (with help) to wipe out the RedBoot bootloader, and was then advised to use the "Advanced Toolkit" to reflash the boot.
The installer (possibly a little too old) was the file "FSL_ATK_TOOL_WINS_STD_INSTALL_1_68.exe". I've looked on Freescale's site and there doesn't seem to be anything newer, AND this isn't linked from the i.MX53 page, only the i.MX27.
The installation went and installed some USB Drivers. That's always a sign of problems.
The Toolkit wouldn't work. It couldn't find the i.MX53 at all. The interface implied it might work with a Serial Port or USB (it let me select Serial), but that didn't work either.
Then I found that it had also wrecked my existing installation of the drivers for the P&E Micro USB ColdFire Multilink. They both use something called "Jungo", but they seem to be mutually incompatible.
In the Device Manager on my PC, the "Jungo / USB Multilink 2.0" icon had the yellow triangle next to it.
Luck for me, the "System Restore" was able to put my computer back before the failed install.