This started happening a few days ago and has me extremely confused.

Whenever I go to shut down my computer, Windows will shut down and my monitor will go blank (signaling that it indeed shut down). But my hardware stays on, my fans still spin, my GPU/PSU's fans still spin but the computer is technically "off" as the power button LED itself is off, no power to the mouse/keyboard either as their LEDs/lights don't turn on.

Flipping the on/off switch on the back of the PSU obviously turns it off, but when I switch the PSU back to on, the hardware starts up again. Windows doesn't start until I press the power button in the front, but the fans/GPU/PSU keep spinning immediately after I turn on the PSU.

I'm completely stumped as to why it's happening, I built this computer over 18 months ago and haven't had a single problem with it until now. I can still boot it up with no problem but the fact that it can't fully shut down/odd problem with starting up is driving me crazy.

Has anyone had anything similar to this before?

What power supply?

Thermaltake 550W.

Not a very good brand. I would certainly suspect that first.

Other possibilities would include a short on the MB... did you install only the MB stand-offs that aligned with the screw holes in the motherboard?

Drop any screws?

The idea that this just started would indicate that either you accidentally loosened/dropped something, or a part failed. If a part failed it's likely the cheap PSU.

If your computer doesn't have any problems booting or while running under load I would think this is more a motherboard problem than a PSU problem. I would guess your MB is failing by not telling other devices to power off when you hit shut down.