I've tried to update one of my test/service partitions that had ArcaOS 5.1 with the USB stick. Phase 1 continued, but after reboot from harddisk for phase 2, it can't find the USB stick anymore.
That can happen, IF you were using a pre=release version of the USB drivers (where did you get ArcaOS 5.1, it hasn't been released to the testers, yet). Due to the way the drivers are versioned, release 12.7 GA is a lower (or equal) level than USB 12.7 test versions. so they don't get updated.
I have done updates from all of the previous ArcaOS GA versions (with no updates to them), and every one of them added the new USB stuff, INCLUDING the XHCD driver. I could not install from USB3, because USB3 is on an add on card, that BIOS does not know about. Trying to update with the pre-release USB 12.7 driver failed to update the driver, and did not install the XHCD driver. FAT32, and ACPI may also fail, under the same conditions. Just install the updated versions from the DVD, and don't mess with test versions, if you don't want this type of problem.
The problem was with the config.sys, The update modified this:
REM RUN = C: \ OS2 \ ACPIDAEMON.EXE
RUN = C: \ OS2 \ ACPIDAEMON.EXE
That is NOT a problem, It is supposed to happen that way. The end result is supposed to be a "new" install of ArcaOS, with most (if not all) of your software still installed.
If ACPI is causing trouble, and you can create a test case that demonstrates the problem, open an incident, and get it fixed. If this is a newer system, it probably doesn't run properly without ACPI. If it is an older system, it may have flaws in the ACPI support (well, new systems can also have flaws in ACPI support).
If that stick was connected to XHCI (USB 3.x) and your old installation had not upgraded the USB drivers to support XHCI before, then this result is (sadly) expected.
This was true for ArcaOS 5.0.5. It is not true fro ArcaOS 5.0.6. See above.
Sure, but no, it wasn't. I've used the (black) USB 2 ports. And the XHCI driver was installed, what makes me wonder for an update, because it was communicated otherwise. After that, I tried a new installation on that partition. Same problem: USB stick can't be found in phase 2. Now I really have to burn a DVD.
USB 2 ports are not always connected to an EHCD controller. They can be connected to an XHCD controller. If the USB stack didn't get updated, for some reason (see above), it is likely that the XHCD controller didn't have the driver.
Looking through the 5.0.6 changelog I see no reason to bother with installing 5.0.6 from dvd, I'll just update my 5.0.5 installation with the few odd drivers that have been updated.
That is probably the easy way. Hopefully, Arca Noae will get their versioning in order, so this doesn't happen again. You should be able to just re-run the update (start from the first boot), to be sure that you get all of it. If you have test versions installed, they may need to be updated manually.
5.0.6 cannot be installed from USB here. Same problem as 5.0.5 - USB stick goes "missing" after the boot "Menu for own choices", not sure if this is what Andreas calls "phase 2" but I would say that it craps out before phase 1.
That is the pre-boot phase. Phase 1 is after it starts to write to the disk drive. If phase 1 works, the USB drivers are working, and the problem is likely that you are using some USB drivers, that are, incorrectly, recognized as being current, when they are not.
If you don't get to the pre-boot menus, it is likely that the BIOS is not reading the USB stick properly. Do you see the dots, as it loads MEMDISK? That is all done by BIOS. Check for a setting that is called something like FAST START, in the USB section. If you read the details, that can either turn off all devices, or it can set it to use only mouse and keyboard. The USB stick will not work, although I would expect the initial menu to also go missing.
BIOS handling of USB boot is absolutely ridiculous. It seems that every machine (even the same brand) does it differently, and user settings (not necessarily made by the user) will affect what happens. I can't even begin to tell you what the settings should be, unless you have a machine identical to one of mine. Look carefully, and read what the settings do. Even then, it may not make any sense. You also cannot boot from an add on card, that the BIOS doesn't know about. If all of that doesn't help, open an incident.