You may want to look into this problem and troubleshoot your memory module slots. While you may believe yourself to have resolved the problem, simply by not using a slot, and while it is very possible DIMM SLOT 1 could have been damaged during assembly, you may be experiencing performance issues from problems with this motherboard. Any time a part of the system fails like a RAM slot, you are going to need to view the other components as suspect as well. I would consider thoroughly checking the first slot for any signs of physical damage, wear and tear, or most importantly, any kind of build-up of dust or material on, in, or near the slot. Obviously, you will know that a can of compressed air is one of the best ways to clear the slot, but even a tiny, nearly microscopic piece of conductive material in the slot can make it temporarily unusable. Permanent damage to the slot could mean permanent damage to other areas. Any damage to the northbridge of the board is not a good sign for longevity, and you should try to clear this issue up. One of the reasons it is recommended that you always use SLOT 1 and 2 (or in some cases this is referred to as 0+1) is to get the best dual channel performance. It is possible you can still get dual channel using 2+3 (or in some cases 1+2 as it is called when you have 0-1-2-3), but you would want to confirm you are able to achieve it using this method.
When you update your BIOS, it is important to clear the CMOS, especially on Gigabyte boards, using @BIOS, and then fixing your settings. Usually Loading Optimized Defaults after a BIOS update is a good place to start, and then configuring as needed from there. I am quite sure you do not need to worry about incrementally updating the BIOS on a Gigabyte board: The BIOS updates are a complete flash and the only problem you could possibly encounter is if you did not clear the CMOS (i.e. go back to factory defaults) after the procedure. If you know you did, it would be difficult to justify a BIOS update as the cause of a new slow down, unless some critical change has been made or you have not optimized your BIOS settings after the flash.
With the latest NVIDIA drivers, you should also not notice a new slow down or choppiness. The unified driver updates that they publish are focused on reliability and performance enhancements for so long as your dedicated graphics card is still supported. It seems that your problem is maintaining a sustainable reliability with your card. If framerates are bouncing up and down in games, you should make sure that the graphics card is not being choked by a related problem. In many cases, this can even be hard disk I/O performance while the game is running.
With the cause of the BSOD unidentified, I am just shooting some troubleshooting tips your way based on the configuration I am able to observe from here. If it was my system, after performing driver maintenance, I would begin running benchmarking and stability tests to see if the system can handle it. This would include running prime95 and memtest86+, but mostly I would recommend you try the AIDA64 trial benchmarking options to evaluate how fast your performance is compared to other video cards and memory modules in your class. This is a good, simplified way of establishing a baseline when trying to identify where the slowdowns are taking place. Combine that with the AIDA stability test, you should see if your rig can go for awhile without bricking down to another BSOD. If you can pass 3dMark11 Basic or Frybench with your card and see if you can get through it without an extreme slow down, you will have a better idea of what type of problem you are looking at with these tests. Many BSODs are memory or temperature related when no hardware issues are immediately apparent, and this is something to take into consideration, whether it is the on-board graphics memory or the module issue you mentioned in passing.
