After a lot of thought and perusal of the article, I've come up with a potential answer.
The 15 pin D-SUB to USB struck me as a strange choice until I realized that the pinout probably set the behavior of the controller. The black box on the cable is just a magnet to supress EMI. The real magic is inside the 15 pin connector. He probably set it up one of three ways or some combination of them.
The most obvious is that the pins are grouped for their functions. 2 set aside for USB PC, then clusters for PS1/PS2, Xbox, GCN, etc. But this is a poor choice for future proofing.
Alternatively, two or three lines are set aside for a small IC inside the D-sub shell that transfers config information about that specific cable. Conceivably, this technique can be use to update internal firmware. The ulimate in futureproofing for entirely new consoles with radically new interfaces. This is expensive though and customers might balk at the higher cable prices.
An intermediate solution is to set aside a collection of pins and simply jump them to change the I/O behavior. For 4 pins with binary logic will net you 16 possible configurations. Using ternary, that goes up to 81. With his love for analog I/O, I absolutely see a possibility for even more configurations just from 4 pins.
All of the above jive with my assumption, you need the PC cable, not the PS3. The hint is in the article you cite, the box comes with, amongst other cables, a USB PC cable yet mentions that the PS3 is forthcoming and can be ordered. The next hint is your mention that the cable you have is labeled as PS3. Why not PS3/PC? Same damn connector right? Go back to the article. It mentions that the analog controls are only available with the consoles that support it eg, PS2. It explicitly mentions that the PC cable disables the analog functions and to regain it back a PS2 adapter must be used.
Logically, since nearly all my PS3 games require the analog, it stands to reason the PS3 cable activates the analog function which Windows does not like or understand. Whereas the PC cable does not. Therefor both cables have a different pinout on the 15 pin side.
You need the PC cable or reverse engineer the pinout and make your own cable.