Welcome to Bleepingcomputer!
You're saying from what I gathered that you have entered your BIOS setup utility and enabled legacy USB support, but then it does not work from time to time.
Is your CMOS battery saving the settings in the BIOS? you will know if this true if your time and date have to be corrected each time you start up your computer. If not you need a new CMOS battery.
Make sure your USB devices are hooked up to the ports on the motherboard's on-board USB ports for the best results.
Make sure your USB ports are not damaged and the plugs are making a good contact.
If all else fails, you can get a USB add-on card and use an unused PCI slot.
Edited by MrBruce1959, 23 April 2010 - 05:04 AM.