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Yes, I've found USB 3 and above to be significantly less compatible and reliable than 2.0 and below. I can always trust that whatever I have plugged into a 2.0 port will work the moment the PC comes on, be it a flash drive or a DVD drive or a keyboard/mouse. That isn't always the case with a 3.0 port.

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The reason for the problems like you describe is that on many motherboards ports with later USB versions were implemented with discrete USB host controllers or ever hubs, while ports of older standards were integrated into the southbridge. This is one of the reasons why the first thing I do encountering a previously unexplored PC is looking on motherboard block diagram in the motherboard's manual to understand how ports are routed.

It was a usb 3 port. It just would not see it to boot.

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