3.Before you start.....
I. If your system supports Intel Hyper-Threading technology, please kindly disable the function in the BIOS.
II. Please close all applications and TSR (such as anti-virus program) under Windows to avoid unexpect error whiling BIOS update.
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I'm not sure if it's now working ok or not (Bios wise) If it is then just leave it nowso should I update it again?
Your motherboard has 3 different revisions, all of which use the same BIOS image file and as kimsland stated, you don't run it from Windows, there is no way it could've ran from within Windows even if you double clicked on it, the BIOS download for you motherboard is a self extracting file, it's name is motherboard_bios_ga-p35c-ds3r_f12e(4).exe which unzips the three following files autoexec.bat, FLASHSPI.EXE and P35CDS3R.12E once double clicked, then there are few steps to take that we have not explained yet.
Install and Remove
CPU-Z does not need to be installed. Just unzip the files in a directory and run the .exe. In order to remove the program, just delete the files.
The program does not copy any file in any directory, neither writes in the registry.