This does seems quite weird but may happen. Never knows, these are logics.
Anyway, if this method has failed, please can you try using a different method.
You can try either:
i) the iflash method by using a Bootable USB pen drive
ii) the recovery method using a normal non-bootable USB pen drive
Download the corresponding bios update: http://downloadcenter.intel.com/Detail_Desc.aspx?agr=Y&Inst=Yes&ProductID=3018&DwnldID=17746&strOSs=38&OSFullName=OS%20Independent&lang=eng
Follow the instructions on the readme file to be able to do the bios update by these method successfully: http://downloadmirror.intel.com/17746/eng/BIOS%20Update%20Readme.pdf
Please note: Using the recovery method you need to remove the BIOS jumper and then do the bios update, then after update power off the system when prompted, put the jumper back to the normal position and then start the system.
Also, for the receovery method, only the downloaded .BIO file should be on the media (nothhing else).
Location of bios configuration jumper can be found on the motherboard manual: http://downloadmirror.intel.com/17746/eng/BIOS%20Update%20Readme.pdf
Hope this will be helpful.