Tim,
I used to own an "un-plaqued" 996R from new, and as a result have done a fair bit of research into why and why not this happened.
Originally, the 996R was a homologation special. In order to compete in WSB, Ducati had to build and sell 150 of these machines that also had to be inspected by the FIM prior to being allowed to enter the series (you may recall the FP-1 missing out on its first year racing because they weren't produced in time for inspection).
In order to make this process financially viable (nevermind that it also helped generate some $$$'s) the factory planned to produce 500 bikes in total. 350 to be sold entirely over the internet, 150 to be reserved for race teams.
The two production runs were ever so slightly different, the bikes reserved for race teams differed in cylinder head design. IIRC there is a different microfiche detailing these changes that is available to dealers.
The day the road bikes were released for sale via ducati.com, the entire 350 road bike allocation was spoken for.
The take up on the 150 race team reserved bikes was, however, a little slower. Teams were less keen to part with so much money for a new engine in a product that was still able to win in WSB.
Seeing the race reserved bikes stacked up in Bologna, someone took the decision to offer a limited amount of these for sale to the various importers.
There was not a second run of bikes - the sandcast process used for the engine cases of the 996R was never intended to produce anymore than the planned 500.
This concludes todays lesson fella!
Any other q's give us a buzz mate.
Cheers!