Biodiesel comes in many formulations, all refined from vegetable oils.  These blends are meant to optimize your performance in the area you buy the fuel.  Vegetable oil is plentiful and cheap but burns 20%-25% hotter than petroleum diesel fuels.

Diesel is intended to detonate, unlike gasoline.  It goes by Cetane rating, which means the harder it explodes in the cylinder, the more power it produces, and the more heat your radiator must dissipate.

The problem is when you add biodiesel to petroleum diesel: it is necessary to retard the injectors 1.2-1.3 degrees before TDC and sometimes replace the injection pump to deliver less fuel to get the biodiesel to burn completely.  If you don't do that, you get carbon monoxide in the exhaust, as the result of incomplete combustion.  If you lean out the mixture too much, you then get NOx emissions, from the nitrogen in the air combining with the oxygen in the air. 

Caterpillar and GE are experimenting with fuels that add just a bit of NH3 to the fuel to react with the NOx: it smells like ammonia, because that is what you're getting instead of nitrous oxide.  I don't know which is worse: nitric acid in the air from all the NOx, or ammonia.  Put one cloud into another and you get a neutral salt: NH4NO3 -- ammonium nitrate.

Burning pure biodiesel gives your petroleum diesel engine heating problems, so cut back the fuel to manufacturers specs for biodiesel to get the most mileage from your fuel.  That and talk to maintenance about putting on catalytic converters to the buses to reduce the CO emissions if they are unwilling to install the new pumps.

Since 2008, Detroit Diesels come with catalytic converters and sensors that tell the engine if you are using biodiesel mixes and will adjust the mixture automatically when it senses CO in the exhaust.