Black smoke on Biodiesel, with no black smoke on #2 doesn't make sense. B99 normally makes about 70% less smoke with the engine running at it's smoke limit. I've seen numbers close to that regardless of the combustion chamber type in every diesel engine I ever fooled with. I've seen Bio make white smoke on older diesels with lower compression ratios(even seen an old Oliver tractor that wouldn't start on it), but I've never seen black smoke simply from switching fuels.
Is he seeing visible smoke or is he just loooking at the tailpipe and seeing the soft black soot building up at the tailpipe tip, and assuming it's smoking more?
The only other thing I can think of, is if the injection pump or injectors are a little worn, switching to Bio improves injection efficiency on some engines. Bio has a high bulk modulus(it's less elastic than #2 at injection pressures). It is pumped more efficiently by the injection pump, and is delivered to the combustion chamber sooner. This results in advanced timing, one of the reasons for Bio's higher NOx emissions. If you think this might be it, lower the smoke limit a little and see if it clears up without a large power loss. If he has his pump timing bumped up already, try backing it off to stock settings and the smoke should go away.
Good Luck,
Joe