Ubuntu only uses some of my USB ports on my motherboard

Ubuntu only uses some of my USB ports on my motherboard

First of all, I have pretty much no experience with Linux whatsoever,
other than trying to install it every once and a while. This time, I've
installed it along with Windows 7 so in case something like this happened,
I would at least be able to use my computer. Now that that's out of the
way, I'll tell you all my problem.
My computer had a history of being incompatible with Ubuntu (tried with
12.04, 12.04 LTS, and now 13.04). Right now, I can only use 2 of the 10
usb ports on my mobo (full hardware list down below). This happens every
time I successfully install any distro of Linux. I'm hoping it is a
problem with my motherboard and an update of the BIOS will fix it. Anyway,
here are me full computer specs.
CPU: AMD FX-8350 4.0GHz 8-Core Processor
CPU Cooler: Antec Kuhler H2O 620 Liquid CPU Cooler
Motherboard: Gigabyte GA-990FXA-UD3 ATX AM3+ Motherboard
Memory: PNY Optima 8GB (2 x 4GB) DDR3-1333 Memory
Storage: Western Digital Caviar Blue 1TB 3.5" 7200RPM Internal Hard Drive
Video Card: XFX Radeon HD 6570 1GB Video Card
Case: Corsair 400R ATX Mid Tower Case
Power Supply: Thermaltake TR2 600W ATX12V Power Supply
Ubuntu detects my usb slots, but some of them as 1.1 instead of 2.0.
If I'm missing any info that would help anyone, please tell me and I'll
tell you as soon as I can.