I thought I would have been through the worst after yesterday (memory trouble), but there is still a major issue with the USB ports.

My setup:
E6400
Asus P5B
2Gb DDR2 800Mhz
7900GTX
480W Tagan

Windows is now reporting in a little pop up bubble "USB Device Not Recognized. One of the USB devices attached to this computer has malfunction, and Windows does not recognize it." When I click on the bubble, it list one Unkown USB Device in bold print.

Strangely though every now and then Windows loads without problems, and I have been able to work for hours. But then, when booting up again some other time, the screen remains black for minutes before Windows comes up and the this message is displayed. Sometimes it also affects my Logitech DiNovo (which is a bluetooth hub/mouse/keyboard), which makes the mouse/keyboard freeze after a minute or so.

Earlier, when connecting several USB devices, Windows also complained that I connect a USB 2.0 device to a USB 1.1 port, and that it could work faster if I connected it to a USB 2.0 port. Of course, all ports on my computer ARE USB 2.0.

I did install the latest Intel Chipset Utility, which from the looks of it does do (improve/fix?) something to USB ports, but god knows what.

So, quite serious USB problems, and I'm stuck once more!

Any help greatly appreciated, as always!

You probably need to install the motherboard drivers for the unknown USB devices.
Also make sure you have enabled in the Bios all the options for USB, such as legacy support, 2.0 support, etc.

As far as I can tell the BIOS has all the right settings.
I'm not sure what you mean with a MOTHERBOARD driver for USB device. A Windows driver? Even if there's a missing driver, it should just report that it couldn't install the device and that's it. But that bubble that I'm getting doesn't shut up and keeps bubbling all the time!

Yes, I mean Windows drivers.
Do you have a USB hub?
If so try disconnecting it.

You could try to identify the offending component by using this:

Unknown Device Identifier (Freeware)

http://www.zhangduo.com/udi.html

The problem is also of a more general nature because even if I only have my mouse/keyboard connected via USB, Windows reports the "device has malfunctioned" message. Apparently the offender is a USB Root Hub.

I would use a driver cleaner, uninstall the chipset drivers, then reinstall the latest drivers from the asus website. Once that is done and you reboot you will probably see a dos shell and it will say something about updating the usb (forgot exactly what it said, thats just what mine did though). Hopefully after doing that things should be good. I had a small problem with mine and took these steps to fix it. My problem was I get into a hurry and install more than one thing at a time.

If that is not the problem see if it is just one port that is affected and it could be that it is bad or you have it hooked up wrong inside. Did you use the q connector that came with the board? Just a thought though, hope you get it working. I just got mine running last night. The motherboard manual seems incomplete, I know it doesn't list important info such as if you want to run dual channel with two sticks you have to put 1 stick in the black and 1 in the yellow. Little things like that make the manual almost useless to a novice.

That sounds very interesting! I never heard of a driver cleaner... could you point me in the right direction where to get one?

Also, I don't think I have a Q connector... what does it do? How does it look like?

You should have q-connectors - they came with the motherboard. It is essentially a bridge between all the little cables that need to fit just so - and the pins on the MB. There was a q-connector for the reset, speaker, ect. bundle, and there was one for USB. There were additional USB pinouts - but they only provided one USB q-connector (at least in my MB).

The purpose of the q-connector is to get all the cables plugged into the bridge, then connect the bridge to the MB - if you are like me, it can get a bit tricky and I have had to use a needle nose pliers or a tweezers in the past.

Hope this helps.

http://www.drivercleaner.net/
if that program doesn't work for those drivers just try reinstalling.
The motherboard comes with 2 small blocks approximately 1"x1/2". One is for 2 usb hookups and the other you plug you case wires (led, reset, power on) to. Then you attach the block to the motherboard. It makes it a little easier to plug everything up right.

Oh yeah I know now. While the one for connecting things like the power button, LEDs etc is very useful I didn't bother with the USB one, as I don't find the appropriate place(s) difficult to access on the board. And all it does is replace but not change the original pin layout, right?

correct on not changing the pin layout.

That program doesnt seem to have what I need... The only Intel bit is "Intel Extreme", which I tried, but it had no effect.

Sorry about that, just try a reinstall of the chipset drivers.

I've tried a reinstall, but it won't do anything. I don't think it's trying either it goes from INSTALLING - to FINISHED in one instant. I know it's a fairly fast CPU. but not THAT fast!
Shame there's nothing to UNinstall.