System very unstable, chkdsk has no effect

[Borealis]

Recently, after running some NN experiments while streaming for 3 days, the system started to slow down and it couldn't even handle Rice (an N64 emulator frontend), which is designed to be run on older, weaker hardware.
Then, my computer couldn't run Illustrator at all and Photoshop caused CPU fan to rev up and down.
After that, my computer restarted and produced continuous stream of short beeps until I removed one of the 4GB sticks in the system (removing all of RAM produced normal "No RAM detected" beeps)
I thought it was the end of it, until...
My graphics card started acting erratically.
It kept going black screen if ANY game is turned on (HeavyLoad test did not crash the computer) and there were noticeable frame rate drops.
The frame rate dropped to 25FPS maximum, while in the past it gave me solid 60FPS even with games like Overwatch and Witcher 3.
I even changed PCI-E slots from original slot to another, to no avail.
I removed the graphics card and switched to internal graphics, but the symptoms got worse -- Now system totally locks up, requiring hard reset.

Detailed and concise report:
- Computer gets unstable after streaming and using programs to experiment
- Computer slows down when programs utilizing graphics card are running
- Flickering screen was observed when graphics card slot changed
- System now locks up when games are running, unless they do not use 3D graphics
- Normal system use, such as using Excel or watching YouTube videos do not lock up the system
- When locked up, system does not respond to any input and hard disk drive activity light goes off and stays off until reset
- Erratic symptoms, it sometimes shows up and sometimes does not
- NEW SYMPTOM: Beeps when moving, clicking or scrolling mouse, computer lags VERY hard while beeps are playing, keyboard still works, system is stable after log-off

Specs:
CPU: Intel Core i5-4690 @ 3.50GHz [NEW PART, Boxed]
RAM: Samsung PC3-12800 8GB RAM (Samsung M378B1G73DB0-CK0) [NEW PART, Bulk]
Samsung PC3-10600 4GB RAM (Samsung M37B5273DH0-CH9) [USED, disconnected]
Samsung PC3-12800 4GB RAM (Samsung M378B5173QH0-CK0) [USED, disconnected]
Motherboard: Gigabyte B85M-D3H (Intel B85 chipset) [NEW PART]
GPU: EmTek NVIDIA GTX760 Jetstream 2GB GDDR5 [NEW PART, disconnected]
Intel HD Graphics 4600
PSU: FSP FSP600-50HPN 600W PSU
HDD: ST3250410AS
ST3160812AS
ODD: HL-DT-ST DVDRAM GH24NSC0
OS: Windows 7 Home Premium x64 SP1

BIOS version is latest (F15)

Build Date: November 2014 ~ October 2015

Tried fix (in sequence):
- Reboot (no effect)
- Power cycle (no effect)
- Physical power disconnect (no effect)
- 10-minute wait then cold reboot (no effect)
- Removed all but 1 RAM stick (1 faulty RAM rejected, system still has problem running games and applications)
- Changed PCI-E slot (card shows flickering image when OS shows "Welcome", black screen, system is interactive)
- CMOS reset (no effect)
- Removed graphics card (Now system locks up completely when it crashes)

- Ran sfc /scannow and chkdsk C: /f /r (no effect)
 

Programs and games that cause crash or doesn't work correctly:

Adobe Illustrator CS6 (black screen/doesn't start)

Adobe Photoshop CS6 (crash when zooming in and out fast)

Witcher 3 (system crash)

Garry's Mod (black screen/crash)

KeyShot 5 (system crash)

Rhinoceros 5 (system crash)

PowerPoint (crash when starting presentation)

 

Edited September 29, 2017 by Borealis
Updated for clarification

[ARikozuM]

Drive SMART data. Do you have anything valuable on the OS drive? If you do, back it up and try a clean install.

[Gumi Rokkaku]

Are you sure all your ram is good?
I'd also try a clean OS install, as mentioned above.

[Borealis]

1 hour ago, ARikozuM said:

Drive SMART data. Do you have anything valuable on the OS drive? If you do, back it up and try a clean install.

SMART shows no errors. All two of them.

[Borealis]

56 minutes ago, Gumi Rokkaku said:

Are you sure all your ram is good?
I'd also try a clean OS install, as mentioned above.

As far as I know, yes.

Computer still screws up even with other OSes.

[Gumi Rokkaku]

I'd double check your ram. Bad ram can cause all kinds of weird problems.
Memtest86 works pretty well. 

[Borealis]

2 hours ago, Gumi Rokkaku said:

I'd double check your ram. Bad ram can cause all kinds of weird problems.
Memtest86 works pretty well. 

I will try that. I really hope it's nothing serious; My family had enough hard time already, and I don't want to add another hardship on it.

 

p.s. I heard that continuous short bursts of beep might mean the power supply has gone bad, or RAM stick has gone bad. But I don't have any known good power supply or test hardware to verify my power supply is good!

[Borealis]

Alright, the results are in:

All pass (10600 one didn't pass)

But the system is still unstable.

[HiImDed]

it might be the mobo because every part that is causing these issues is dependant on the mobo

what im trying to say is your mobo might be faulty

[HiImDed]

how old is your mobo? and when did it start? I would try to also install a older bios to see if that helps.

[Borealis]

5 minutes ago, HiImDed said:

how old is your mobo? and when did it start? I would try to also install a older bios to see if that helps.

See build date. The problem started AFTER the experiment crashed, which used lots of CPU.

[HiImDed]

i still am going to guess it is a catastrophic failure in the mobo

[Borealis]

14 hours ago, HiImDed said:

i still am going to guess it is a catastrophic failure in the mobo

That could be the worst thing that could happen. I will keep testing this build to see if a specific action (other than opening up a bunch of programs) causes system lockup/crash/freeze.

[Borealis]

Okay, reseated literally EVERY SINGLE removable component, cleaned up EVERY SINGLE contact points and made sure to test each component separately, and came to the conclusion:

 

[Borealis]

...Now it's okay for some reason? I honestly don't know what just happened.

 

So, the conclusion is that "It fixed itself"...

 

EDIT: It died again, and I now suspect the graphics card is borked. I'm sending this off to the manufacturer for repair once the holiday ends.