Weird USB Problem

Heya, I've got weird USB problems, and can't seem to work out what's wrong.

I'm using Windows 8 x64, all updated, which had been working without problem for about 8 months now.

I noticed my internel card reader drives (9 pin USB header) kept disappearing and reappearing quickly, in both My Computer, and Device Manager. So I assumed it was dying and bought a new one, but it too did the same thing, so assumed it must be the USB connecter dying, and left it unplugged, and orderd an external card reader (yet to arrive).

Sadly my USB flash drives and USB hard drives started doing the same thing, front and back ports, these drives will disappear and reappear a few times then work as normal, weird thing is my USB printer, mouse, keyboard, and Sansa Clip+ work fine.

I tried testing in WinPE v4, and Linux (Ubuntu LiveCD) and everything seems to be working fine, including the internel card reader. So I reinstalled Windows 8 after trying fixes like uninstalling the USB Root entries in Device Manager, and messing with the USB power saving options in Windows, even though they're at the defaults and never caused problems before, but the internel card reader was doing the same thing again before even doing any updates, or installing drivers.

I have found a workaround for the reader, if I disable it within Device Manger before putting a card in, and then enabling the device it works, but once ejected it goes back to disappearing and reappearing again.

The PC is a Dell Inspiron 531, yep it's old.

If all the usb peripherals work using the WinPE and Linux live cd.....that tells me it's not a hardware issue. This means a few things, it could be a software related issue which could be anything from a missing/corrupt system file to an OS update. The other thing is a Virus or a bug of some kind which are known to disable such input connections.

I'd check your system for a Virus, trojan, worm with any all the software you have.

Also, check for said issue in safemode.

Hmm, but I did say I reinstalled, and the problem was still there before doing any updates, or driver installs. The medium used for the install worked before without issue, and I even reburnt the ISO, after checking its hash to make sure it wasn't damaged.

Install medium is a ISO created with Windows8-Setup, when I did this I hashed the ISO.