I do not know of anything that could do more about diagnosing your problem that you haven't done. There is software that would measure your transfer rates, but it seems you already know that. Since everything necessary is set up correctly, there is still something that is not recognizing the USB 2.0 devices. A new motherboard may be needed.
Before you do that, perhaps blow out the unit in case some dust might be causing a problem. Before you decide to replace the motherboard, you might want to try unplugging the unit and use whatever procedure ASUS recommends to reset the bios. Some boards have jumpers, some systems seem to be able to hold the power button for several seconds or whatever else. Resetting the bios to it's defaults might even help, but make note of your settings before you do that or the other procedures. There is always a chance some glitch in the bios is causing the problem.
Maybe someone else will have another suggestion ....