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USB Malfunctioning

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Hello,
I've been having this problem for quite some time now.

It seems like my USB ports have malfunctioned or some sort.
I don't exactly know what did I do when it happened, but everytime I turn on my PC after a long power-off state, the USB devices does not function immediately.
The first boot-up will recognize the USB devices, such as mouse, keyboard, harddrive, hub, etc, but I can't use any of them after it gets to the Windows welcome screen, like mouse won't do anything, can't type anything, etc.
At that state, the only resort is to restart the PC, the second boot have everything works "fine" so far, with additional note that I have to unplug-replug some devices like wi-fi adaptor and hubs in order to get them work again.


So far I have tried these methods:

1. Unplug-replug not working devices during the issue.
2. Reinstalling Windows.
3. Resetting BIOS by using the CMOS battery method.
4. Cleaning and reseating the hardwares.
5. Remove one RAM at a time.
6. Remove any USB devices before boot-up (as in booting up without any devices plugged in).

Everything has come up with no luck at all, the error doesn't even seem to go away.


Also some things to note:

1. Apparently the problem starts roughly 1 hour after shut down, just found it out today.
2. Several days before this problem exist, I bought a WD Blue 1TB and installed it immediately. Also did reinstall Windows two times after installing the harddrive due to trojans (they infected my old HDD which is used for the OS atm, not the new one).
3. There's 2x case USB port and 4x motherboard USB port. I didn't have to replug the USB devices that is connected to the motherboard USB ports, but I have to replug the devices that connects to the case USB ports.
4. I suspect this is a motherboard issue since the motherboard is old enough, but is it possible that this is a PSU issue? Actually hope it's a motherboard issue though, I can't afford to waste money on another PSU.


In case it's needed, my PC spec:

PSU : RAIDMAX RX-500AF-B
CPU : AMD Athlon II X3 455
GPU : AMD R7 240 2GB GDDR3
Mobo : BIOSTAR A780LE
RAM : DDR2 1GB + DDR2 2GB
HDD : 160GB SEAGATE Barracuda (ATA) + 1TB WD Blue (SATA)


Any help is greatly appreciated, also thanks in advance !

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