Well, having used a lot of biodiesel I can tell you a few things
1) Towcat is right...any natural or butyl rubber will eventually be eaten up by biodiesel
2) Dealers discourage the use of biodiesel because they don't know much about it and higher blends of very bad biodiesel may damage fuel injection systems
3) Its pretty likely the fuel injection system that you are risking not the engine with biodiesel. I have had zero engine trouble in more than 30,000 mostly B100 miles. I have had to replace an IP and a set of injectors in that timeframe, but I think that was more due to a poor build and being repeatedly run out of fuel(don't ask) than bio per se. Also they'll try to discourage you from running B100 because any fuel damage won't be warrantied...well they won't warrant any fuel damage from D2 either...but usually you have a big oil company or at least local distributor to go after. If it's homebrew, you're to kicking yourself in the tail and eating the cost, or going after the local hippie biofuel co-op if commerically bought.