I just know that I've read that for some people a powered hub took care of the issue. Maybe it wouldn't have worked for you. I just wanted to give anyone that had the issue one more avenue to try before cutting the cables, although I suppose they could now just disconnect them via those connectors(looks like Molex Pico or JST connectors to me).
My issues were the same when plugged into the front case ports that are connected to my motherboard header, but plugged into the mobo directly took care of the issue, and then the extensions I added are only 3 feet and I only added them due to the aforementioned issue that I can flip a coin as to whether or not the headset is recognized upon opening WMR portal or launching steam VR without having to unplug and plug back in the USB. I'd rather not have to reach fully behind my tower each time, plus I'd rather wear out the female plug on the extension cable rather than on my mobo.
Out of curiosity, did you try changing to a different extension cable? I had also heard that the cable could be an issue, so I bought one that was recommended by another redditor that confirmed worked without issues. I just went back 6 months into my Amazon history to pull the link: Monoprice USB 3.0 Extension Cable. I only needed the 3' one since my office is smallish and I only have an 8' wide x 5' deep play area after moving my desk chair out of the room. The redditor that suggested it was using the 6' cable without a powered hub just plugged into his mobo as well. HDMI is less finicky as long as it's a newer highspeed cable that doesn't increase your run to over 25' at least from my understanding. I just got a 3' Amazon Basics so my USB and HDMI would be the same length.
I wasn't using the Amazon Basics for USB 3.0, only the HDMI. The USB I use was this Monoprice one that specifically lists Oculus VR in the title because it was recommended in a thread by a redditor that said it worked for them. In that same thread people were bitching that the Amazon Basics USB didn't work which was why the Monoprice cable was recommended.
Anyway, sorry I wasn't more clear that I only used Amazon Basics for the HDMI and not the USB.