I have the issue with having to hot plug my USB every reboot. I do not have to rerun setup, it just starts working. I can plug it back into same port or any other port and everything is good until reboot.
I did have quite a few other issues and did the Safe mode with no networking uninstall, clear all cache files etc... That fixed all kinds of weird issues.
Oculus support has been not very responsive to say the least. I think I will be returning the rift s if there is no fix for this USB thing.