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So you fixed your problem by using ScpToolkit?

It shouldn't matter what device. Standards are standards.

Edit:
Your issue is more likely to be related to software hijacking your settings, or software (emus) resetting themselves for some...

USB 2.0 device should work on a USB 3.0 socket. USB 3.0 has additional wires but the wires needed for USB 2.0 functionality are the same.

I don't know what causes it but I've seen this issue mentioned before.
I wouldn't be using DS3 controller for things other than PS3 myself, these controllers definitely aren't easy to replace now....