it wasn’t the biodiesel
As it turns out, it was not biodiesel that was giving my New Beetle TDI issues. According to the dealer, there is a techical bulletin from Volkswagen on these vehicles that implicates a valve in the fuel system as the culprit. The small amout of gelling biodiesel may have simply prompted the valve to fail (causing fuel starvation, which I took as a gelled filter), but the vehicle was prone to that failure regardless of the fuel.
Now, I’m still nervous about using biodiesel in an unheated fuel system. The B100 I got actually turned solid below freezing, so it may have been (and likely was) produced from some pretty heavy feedstock (possibly tallow). All fuel is not created equal! So I’ll stick with petrodiesel for this winter, and consider any fuel heating modifications next spring/summer.
I still stand by my recommendations that you know how to change your fuel filter before you start using biodiesel, but rest assured that it was not biodiesel that was causing the vehicle troubles I’ve been experiencing.
Andrew: Idea Hamster, P.Eng. 
If you need any advice or help with the car, check out the Ontario section at tdiclub.com. There are a few of us using bio when it warms up a bit. B100 in the winter is always a bit of a gamble in my experience. Send me an e-mail if you get a chance as I’m looking for some local info on cohousing projects.