Good- as you know, disk imaging can save you clean installs in some cases- this one was odd.
Out of curiosity, after the installation. what partitions do you now have?
(I assume you created a current install disk if you didn't have one, noting you mention a CD rather than a bootable flash disk).
I don't see how having one partition as system and boot could be causing an issue. It is normal for bios booting. Nothing wrong with that.
If Windows setup.exe detects an existing active partition it doesn't create a separate system partition.
It sounds like bios is taking a while to enumerate a device. Might be hardware issue, possibly poor connection, possibly power supply struggling.
If the problem persists you could try disconnecting peripherals/devices and reconnect one at a time which might give a clue.
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