pghPAtdi,
sure enough, others here have reported smoke after running a few tanks of B100 on a TDI with many miles on petro-Diesel. And here in western PA, some crappy diesel fuel can clogg TDI intakes as soon as 40k miles (this was one case seen by a VW tech).
Most likely, the B100 is loosening up the gunk in various places like the intake, and perhaps the bottom of the fuel tank, etc. A good thing to do is to replace the fuel filter after a tank or two of B100, in case some cleaning was done with the fuel tank. Other than that, step on it and run with biodiesel as much as possible (including blends).
BTW, I would bet that the intake in your TDI could have been somewhat clogged before you got it, because when I drove behind you this past spring I noticed that it would smoke each time you shifted gears. On the other hand, if you remember, I could really revv it up on our beetle and you wouldn't see any smoke out the back. Thanks to many miles on B100 or blends...