well, i would try disconnecting all of the usb connectors on the mobo to see if that makes the usb 3.0 on the rear work. if it does then plug them back in 1 by 1 to see if one of the cables / connectors is causing the problem.
if that doesn't make any different i'd try the mobo outside of the case, maybe a short is screwing with something. really not sure tbh though, does seem like a weird one. i don;t really see how the psu or the m.2 would cause the issue, as long as the plugs are properly in, so my guess would be something with the case.