I have since realized that a few of my unassigned devices have, somehow, lost their 'unassigned device configuration / preferences'.
Strangely, the drives are showing up underneath as configure but disconnected despite also being present in the 'unassigned device' section (identical identifications).
I have a feeling this issue, as well as the initial sloowwww / delayed reboot, could be related to what Frank1940 and others mentioned earlier about the boot order changing in the BIOS:
It was easy enough to reconfigure my unassigned drives so no real drama, but I want to get to the bottom of this, in case it causes me any issues later on (and in case there is actually a bug / issue that could potentially effect others upgrading to 6.3.4). I really have no idea but i'm thinking the drive mapping / ordering is getting messed up somehow? Being the noob I am, I am not sure what I should be looking for regarding my suspicions.
(note, I'm a proper newby so please feel free to pull me up on any incorrect terminology and/or general stupidity )