I don't notice any difference running B100 in my '98 E300TD.
Have you changed your fuel filter? Biodiesel is an excellent solvent/detergent, and it may have washed up sludge from your tank and lines into the filter.
I drove three tankfuls of B100 through my car, then noticed it getting a little sluggish. I changed the fuel filter to a new one, and it's like a whole new car -- ready to run. For about $10, cheap performance improvement.