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The first round of system chipsets that was advertized as having USB was made to an early pre-1.0 USB specification, and shipped in the hope that this attempt would be close enough to the 1.0 spec that the chips would be useful.
After that it turned out that the specification had to be changed bigtime to get it working, and that the chipsets would have to be changed as well. That's why there are mainboards around that seem to have everything you need for USB, yet don't show any sign of actually doing it.
BIOS developers then were asked to hide these pre-1.0 USB controllers, both from BIOS setup and, where possible on chipset programming level (as with Intel's PIIX3 south bridge chip), from the PCI bus as well.
The big four chipset makers Intel, ALi, VIA and SiS all had pre-1.0 chips out. I don't have any detail for ALi and SiS. Intel's pre-spec PIIX3 is recognized by being rev. 0 (as read through PCI revision ID register) and marked "SU052" production S-spec. The rev. 1 "SU093" is the one with working USB. VIA has working USB in the 82C586B south bridge, and it seems the implementation in the original 82C586 and 82C586A was pre-spec, although I don't have confirmation on that (only the fact that Ocean Rhino 12 and PC-Chips M537 boards were advertized as "with working USB" once they sported the 586B).
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