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Windows 8.1 blinking - on startup

Sounds to me that is how your system boots. Probably because you formatted to GPT your drive, but your motherboard is not fully UEFI ready.

It all depends when it happens. You seam to have skipped many steps in your explanation on what happens. What is your full system specs?

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Make sure you have the latest BIOS/UEFI installed.

And make sure you have it set to UEFI mode in the UEFI screen, and not BIOS/Legacy mode.

Is your SSD: GPT or MBR?

Does it go faster if you unplug your HDD?

In the UEFI setup screen, disable all hardware/component you don't use (for example the SATA controllers you don't use)

If you remove your graphics card out of your system completely, and use the Intel integrated graphics, does your problem fixed? (if so I think I know what is the problem).

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