One USB 3.0 Port on front panel malfunctioning

I have a 3rd party 5.25" front panel with two USB 3.0 ports. Each port goes to a single cable that connects to the USB 3.0 20-pin header on the motherboard.

Both ports usually work fine with different USB devices. But for my hard drive enclosure, it connects fine to one of the USB 3.0 ports but not the other. This is given the fact that the left port works fine with other things like USB drivers and game controllers, and that both ports have equal cable length to the motherboard header. So I really cannot think of why this would be happening. The enclosure works fine on the back USB 3.0 ports, so I assume this isn't an issue with the enclosure.

MSI Z97M-G43
i7-5775c
G.Skill 16GB DDR3 RAM
EVGA GTX 1070
EVGA SuperNova 550 G2

The pins are all fine but maybe there is a disconnect in the traces. It's a 2.5" enclosure by Orico which uses a USB C to USB A cable.

I've also realized that the speed is bad on these ports, possibly running at USB 2.0 speeds. It doesn't make much sense because it's just an extension cable from the header to the ports, no extra circuitry like a lot of USB front panels.

It's USB 3.0 but I'm nearly sure it was a connection problem at the 20-pin header. The 20-pin port for USB 3.0 in general is a very poor design especially when it's installed sideways rather than vertically on the motherboard, but even worse is that the port on my motherboard has a plastic shell that easily comes off when you remove the cable from the port. It's quite hard to put it back on and it's possible something about that was causing connection issues.

I was able to temporarily get it to run at USB 3.0 speeds today but then as I went to replace the plastic shell again one of the pins got bent to the point of not being fixable. It may be a blessing in disguise because I'd rather not play the guessing game of whether or not my USB device will work with my front panel USB 3.0 ports. I still have rear USB 3.0 for fast transfers but it's just not as convenient.

There could be a way to use my m.2 slot but I'd need some kind of cable that connects directly to it. The m.2 adapter cards with the USB 3.0/3.1 port attached onto the PCB won't fit underneath my GPU and I can't move my GPU. So it would need to be a low profile direct PCIe to USB 3.0 cable without the extra height that the usual m.2 adapter cards have, unless the port is on the side of the card facing sideways and not up, then maybe I could attach the cable I currently have. I'm also open to buying a front panel for USB 3.1 that connects to the m.2 adapter so I can ditch the absolutely awful USB 3.0 20-pin cable design. USB 3.0 design sucked and the people who designed it were idiots. If anyone has suggestions let me know.

I'm using all of the slots that are able to be used. There is a second x1 slot covered by the GPU, but even if it weren't covered the manual says I can't use more than one x1 slot at a time anyway. So I'd need a way to connect something to the m.2 slot, which I believe uses PCIe x4. I don't do USB hubs and probably never will.

There is something else that could possibly work though. If I can get a wifi card that fits in my m.2 slot, that would free up the x1 slot to put in that USB 3.0 PCIe card. https://static.bhphoto.com/images/images2500x2500/1402225723_1056236.jpg

I'm not 100% sure if a perfectly flat card would fit under the GPU. I'll need to check later.