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I tried a few things but my problem is still here. If I restart my PC, USB devices work well. However, after waking up from suspend, the two USB 3.0 ports don't work but the USB 2.0 ports work well.

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Sounds like a kernel bug, What kernel do you have? What version of Ubuntu do you have? – Alvar Jul 15 '13 at 11:32
13.04, also same problem in 12.04 too.. – Ahmet Erol Ulasmis Jul 15 '13 at 11:45
intel i5 - samsung series 9 ultrabook NP900X4D – Ahmet Erol Ulasmis Jul 15 '13 at 11:46
What Linux Kernel version do you have? look in system information of your computer. – Alvar Jul 15 '13 at 12:53

I solved it going into the BIOS and activating "USB S3 resume" (or something like that) option under the advance tab.

Hope this works for you!

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