The controller's USB is plugged directly into the motherboard. It may need more power than that?
I've had three different U360s and I had to use a powered USB hub each time. One project was a laptop and while I could get one U360 to work perfectly the second simply did not want to know. (Both were plugged directly into their own individual USB ports on the laptop). A powered USB hub solved all the problems.
The third U360 was a single joystick plugged into an Intel Atom 330 Mini-ITX board. Again I needed a powered hub to make it work correctly. It was registering in Windows but as soon as Mala and Mame started the stick didn't work. All the software was configured correctly. Again as soon as I tried a powered hub (in fact the same hub that was on the lappy) it all worked seamlessly. I immediately went out and bought a second hub to get both projects working 100%.
I believe 500mA is the maximum a USB port will give out. And it seems the U360 is right on the borderline of needing this much power. Some people report no problems. Maybe it was the older PC hardware I was using that perhaps was underpowering my USB ports?

The U360s are the best "all round" sticks you can get in all honesty. Buying powered hubs isn't a deal breaker for me.
I'd try and borrow one from somewhere if you don't have one already just in case it doesn't solve the issue. I'm guessing at the powered hub solution because of my experiences.