Boots directly into Windows Recovery but won't recover

Just a few days ago I did a clean install of Windows 10 Pro 1903 (i.e., deleted all existing partitions from within the installer and let it proceed using the entire disk). I've had a couple of failed boots since then where it hangs on the lock screen and won't show the password box, or goes black before showing the lock screen. This morning, it hung on the lock screen, I powered down, restarted, and got "Bootmgr missing." Booted into WinRE from USB, ran startup repair, removed the USB, and now the computer boots directly into the recovery environment. So this is where it's at now, booting WinRE again from USB:

Startup Repair --> Startup Repair couldn't repair your computer.
Uninstall Latest Quality Update --> We ran into a problem and won't be able to ...
System Restore --> To use System Restore, you must specify which Windows installation to restore
chkdsk c: /f --> Windows scanned the file system and found no problems
bcdedit --> Boot configuration data store could not be opened. Configuration registry database is corrupt.
SFC /scannow /offbootdir=C:\ /offwindir=C:\windows --> did not find any integrity violations
DISM /image:C:\ /cleanup-image /restorehealth --> Operation completed successfully
bootrec /fixmbr --> completed successfully
bootrec /fixboot --> access is denied
bootrec /rebuildbcd --> identified windows installations 1 / Cannot create a file when that file already exists
bcdboot c:\windows /s c: --> Boot files successfully created

With USB removed, it still boots into the recovery environment. What's going on?

Desktop computer with Pentium G620, Samsung EVO 840 SSD added as system drive but otherwise totally stock. Was previously running fine on 1803, but upgrade to 1903 failed, which is why I did a clean install of 1903.

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Whoa, just visited BIOS settings and it's not seeing my SSD system drive at all, says that nothing is connected on AHCI Port 1!!!

I pulled the disk out and connected it (via SATA-USB adapter) to another Windows computer and it looks fine. WTF??

If I change SATA mode to Native IDE, then BIOS does detect the SSD, but it still won't boot.

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Aaaaand, now AHCI sees the SSD again, but it boots straight to WinRE as originally described.

As recommended here Boot problems. : windows I booted with Macrium Reflect recovery and ran "fix windows boot problems." Fixed it in 10 seconds. This, after spending all day failing to fix it with Microsoft own tools.