I've used various blends of biodiesel over the years with a couple vehicles, and while I have not noted performance issues like you have, I also haven't been looking for them. It should be noted that it is well known that FAMEs (i.e., the usual biodiesel) have about 10% less energy per gallon than petrodiesel, so a performance hit could be expected at higher blends.
But there is one big benefit to biodiesel: lubricity. There was a Canadian study a few years ago that found that as little as 1/2% biodiesel had a significant reduction in iron wear particles in the engine oil, cutting them by as much as half. This effect seemed to peak in the 1-2% range, however. So if you are concerned about possible wear issues with ULSD, a percent or so of biodiesel is one of the best additives available.
It should also be noted that currently available biodiesels are just the first generation of the fuel. There are other equally renewable alternatives being researched. So stay tuned for further developments.