I'm not sure I understand your post clearly but are you saying your USB Flash stick was physically burned/damaged when you plugged it into one of your boards USB 3.0 ports? If it was a port connected to the motherboard (rather than built into it), the wiring on the adapter cable sounds to be incorrect - you should attend to this with urgency before powering up the PC again. As an interim solution you could unplug such USB 3.0 ports from the board until a compatible adapter is sourced. You should also carefully check that the metal chassis shield around the motherboards rear connectors isn't earthing out USB devices plugging into those ports if that was the port you used.
I connect my USB flash directly to the USB port on the back panel.
Connected with KingTon USB => OK.
Connected with NetApp USB (2GB) and "strange branch" USB (only 512MB) => burn.
Sorry, I still don't understand what the problem is - please explain further (including what this 'strange branch' is all about - perhaps providing a weblink to the product or a picture etc). Are all of your USB ports working fine eg testing them with a multitude of devices?