Hello fellow ASUS users.
I'm going to split my issue into two parts to try and have it make sense somewhat.

The problem manifests like this:
With the previous Windows 8.1 installed and the latest GPU drivers, after logging in, starting an application (for ex., dota 2) would make the app crash instantly, followed by a notification from the taskbar that the GPU driver had failed and recovered. After restarting the application, MSI Afterburner would show my GPU either running at 99% constantly with temps between 70/80 Celsius, or it would display it as throttled down, with 405mhz core speed, and 800mhz memory speed, which makes the fps drop to 20/30.
If I browse the web though, and not start any games, at some random point while using the laptop, the screen turns black for a split second, then turns back on. If I start a game after this happens, the core/memory speed will be at 405mhz until restarting. I kept using it like this hoping that it was a driver flaw that would be corrected with future updates. It did not.

After reinstalling Windows 8.1, with the driver listed in the ASUS driver page for my notebook, I can start a game without any issues and the parameters will be working as they should. However, 6 hours after installing, the screen flickered again, on two separate occasions while using it(not in a game), and made my clock speed lock down afterwards.

After this, I sent it to RMA to the retailer at the start of the week. Today their contractor emailed me that the defect did not manifest, and are currently sending it back to me. This would be the third RMA it had since I purchased it. I got it refurbished but it it was described as barely having the box opened. The first two RMA's were for faulty power connectors, which they solved by ordering another motherboard. The last time it happened, it came back without the keyboard backlight working and I had to install those drivers from a 17 inch model to make it work. Could this mean that the motherboard is actually faulty? I'm also wondering if further usage would make the issue manifest as I presented it the first time. I could send it back then again.

However, I was thinking someone here might help me figure this out so I don't have to RMA it. If it stays like this, I'm thinking to break the warranty and get myself another motherboard.

I don't have the full specs, I will update them with further info when i get it back and whatever else might be required. It is the i5 3210m/Nvidia gtx660m/ 4GB Ram model, upgraded to 8 GB. 500Gb HDD, no SSD.
Also, sorry about the writing, typing off a tablet sucks.

I'm just going to put this here because I just remembered it as I was reading what I wrote. The very first time something bad happened with the GPU was when it bluescreened while playing a game. I did not get to read the error number as it just flashed and restarted and I wasn't expecting that, but I clearly remember it mentioning the GPU driver in the message. Might help.
Cheers.

Also, tried disabling/enabling the GPU from Device Manager. No joy. Also, whenever the GPU crashes, Device Manager lists it as a generic display adaptor.