Good morning. The problem is not that VIA is not performant but when it is working concurently with another USB chipset on the same MTB it creates some minor problems. The Intel works fine just because it is part of the CPU surrounding chipset. The same applies to Ethernet ports. Intel CPU's can only supply one Ethernet Port so the second one depends on another company chipset and Intel supports only 6 SATA ports all others will be handled by other companies such as Marvell.
To make it work you need to tune the bridge between the two. Though USB do not work through a HUB and a bridge it has its own method to work independently (in parrallel not serie) without interfering with one to the other. One on the way to have the VIA USB working properly is to plug-in all your peripherals before installing the OS, though in certain cases I saw it works only by re-installing only the driver, it depends on the OS version. Driver re-installation works under XP but sure under Win 7.
In your last post you say that you are using the front panel USB, those are through VIA headers. I do not know if you have kept your original BIOS version or if you have upgraded it again and again which also sometime makes more problem than it solves. If they do not appear in your CMOS it simply mean that the VIA chipset has not been recognized by the OS and/or drivers are not installled but usually the BIOS has all it needs before installing the OS though there has been exceptions in the past.
Never plug a keyboard nor mouse into a 3.0 USB, it is like opening a garage door to let the cat out, at the worst it could degrade the speed of the entire USB 3.0 layout.
I beleive you should the VIA site
http://www.via.com.tw/en/support/drivers.jsp to find the right driver set. Make sure you also check on the motherboard the VIA chipset number. Beware, there might be two VIA chipset, on for the USB, generaly located near the back USB ports and another one located near the PCI slots and sound chipset. The tool at the address will provide you the exact drivers set for the USB which are different for each OS.
Hope this will help. Cheers