Wanted to pass on some research I've been doing across the web:

Researchers testing a 91 and 92 on biodiesel ran into problems after 50,000 miles on the 91, due to BD degrading parts in the fuel system.[director] They determined that Dodge switched out all nitrile parts, which degrade over time when exposed to BD, after 91. They discontinued the study after they ran the 92 for 100,000, with no problems. The articles list a lot of technical performance information. For those interested:

http://www.missouri.edu/~pavt0689/Research_Needs_Resulting.pdf

and

http://www.missouri.edu/~pavt0689/Project_Update_Fueling_5.9L_Cummins_Engines.pdf

I also discovered concerns by some that high pressure in 3rd generations may cause BD to become stringy, sticky, thick or otherwise bad. Scholarly types concluded that those symptoms were most likely to be caused by impurities or imperfections due to poor-quality home brew, and not BD per se.

Research I've read indicates the polymerization that takes place with BD on common rail engines is due to the feed stock the fuel is made from. The feed stocks that tend to polymerize readily are the oils that are also bad for human health, like animal fat and soy. BD made from fast food restaurants that deep fry with lard is the worst.
No big deal on a CRI engine as long as you don't exceed B50.