|... re-installed the system from scratch...|
"Usually" that means wipe the drive (reformat etc.) and then (re-)install etc...?
How was it done on this occasion? Was it a parallel installation; a repair installation, or what?
And to answer (again) what apparently was the original question...; if the bios does support a boot via a usb device (usually a cd/dvd unit) then one "ought" to be able to use it to re-install an OS... Wiping a drive, reformatting it etc. ought not to affect any usb boot options. And the poster has already stated the bios is set for a usb boot option.
So if all current efforts have failed... ensure only the internal HD is around (no external HD attached - for safety's sake) and reformat it; then re-install the OS - presumably via the external CD/DVD unit?
Reformat can be done via XP setup etc.
On other option not mentioned... Boot up with Linux variant CD and then re-scan system fully - both locally and an on-line scan?
That way the HD is totally an inert structure and if there's anything that is "hiding" as it in its boot sector or dumped down in some way to RAM/cache etc... it may now be inert/inactive; and thus a scan that way "may" eraadicate it?
But personally, if all data is safely off the system, at this time I'd go a full reformat, re-install etc. And maybe even (on this occasion) even use a killdisk or similar routine; or a mid-level format routine (using the HD's manufacturers util to that end prior to it... An mid-level format writes zeros to the drive and effectively destroys anything on it; resetting to as close to factory gate status as is possible?
I can't help the feeling that we're not getting a fully accurate account of what etc. has been done; not that it's intentional - but rather something is being lost in the telling?