This is solved by simply disabling the OS driver's USB 2/3 monitor. There is a conflict between the way the hardware recognizes USB 2.0/3.0 devices and the way an operating system performs the same task. If you read this basic document it clearly shows the problem with the uPD720200, uPD720201, and uPD720202 must be solved by modifying the device driver.
MSI RENESAS USB 3.0 DRIVER PDF
(be aware this is a PDF download file link (the author of the PDF matches the host site "stonegroup" but this is just a link I found while searching DDG)) After looking for potential application notes floating around the web I came across the following. This document has pinouts and timing diagrams but no application notes. However, the complete datasheet is available through parts distributors such as Mouser. The datasheet for this is not directly available from Renesas without first creating an account on their website.
MSI RENESAS USB 3.0 DRIVER SOFTWARE
I am an amateur hardware 'enthusiast' and would have no problem (attempting) troubleshooting the hardware side of this, but my software skills are weak. The following is intended mostly for Devs. This will show the status messages and list things like a failure This will return the status of all hardware on the PCI bus (filter through this intuitively) This returns the status of all system hardware (like a PCIe slot) I have listed my results from these commands at the bottom of this. Here are a list of commands to use if anyone is facing similar issues. All three devices exhibit the same failure mode. I have tested the PCIe card with a USB keyboard (generic so.1.1/2.0?), and both a self powered and USB powered USB 3.0 external hard drive. I have also tested it on Lubuntu 18.04, and 19.04. Below I have shown, my system information, the fact that the hardware is initialized, and finally the output when it fails after plugging in a device. It appears the only answer with others has been "update your kernel." However on the other posts it appears the hardware was never working at all, no real solution was found, and as I will show I don't believe the Kernel version is the issue. The actual product is a cheap Chinese USB to PCIe adapter card or pic of the internal hardware.
I am having similar problems as here and here.
(Edited ~12pm PST May 6th for consolidation and clarity)
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