Seeing this message appear is just a bug in the EBU program. The BIOS likely installed correctly. The message will go away on the next reboot. On this next reboot, use F2 to go into BIOS Setup (Visual BIOS) and check the screen header for the BIOS version. If it says it is version 52, then it installed correctly.
My words of wisdom:
1. In future, do not use the EBU executables. The tool is broken (I have told the developers) and causes instability - like the hang you saw (but you got off easy) - as well as these incorrect messages on the reboot.
2. I recommend that, after updating the BIOS, you go into BIOS Setup, use F9 to reset the BIOS configuration and then make only the changes that you absolutely need (boot order, etc.).
Hope this helps,