Thank you for the detailed test report @bugcity . For the two problems described:
USB 2.0 high speed not working well - it sounds like the peripherals that are not working are all this speed, or are falling back to it when plugged into the black ports since those are 2.0-only. (Low or full speed sounds OK, and super speed is OK.) I had high hopes that the latest tuning improvement would address this, since it did work on the affected device that I have, but unfortunately it sounds like this iteration does not. Still, I appreciate the detailed report and test effort.
USB SATA disk enclosure causing shutoff - this device could be actually overcurrenting the Librem Mini USB ports or +5V rail. The fact that the system will not power on again until power is removed can be caused by this.
Many peripherals play fast and loose with USB power limits, which is OK a lot of the time because many hosts don’t have per-port overcurrent protection, which means they just hope that you don’t damage the system by overcurrenting. Librem Mini does have per-port overcurrent though (one for each pair of A ports).
The overcurrent detection signaling was disabled in this build (the actual protection still applies, just the signaling to the host which was causing some false positives). That helped, but since some shutoffs remain, it seems likely that the hard disk is actually overcurrenting either the USB-A port pair or the +5V rail, which causes the device to shut off to protect itself from damage.
Does it have an option to self-power (plug in a power supply to the enclosure itself)? Could you check the current rating on the disk installed in the enclosure? (Probably says something like 5V 800 mA, 5V 1.0 A, or 5V 0.55 A, something along those lines.)
You can gain a little bit of current headroom by using a particular port pair (two stacked ports) for just this hard disk, leave the other port empty. The overcurrents are shared per stacked port pair on Mini so you can effectively borrow the current from the other port this way, though I’m not sure this will be enough for this disk. Or, if you have a self-powered USB hub that tolerates whatever current this hard disk needs, you could use that.
Thanks again for the detailed report, I hope this helps.