if it is a 5.4 the early 3 valve 5.4s had a problem with injectors leaking and while running will cause an excessive rich condition they also have extended coverage for this problem you very well could have an injector leaking.
running bio diesel will also lower fuel mileage as it contains less energy to release as the same amount of regular diesel, you also might look into using a cetane boost like the motorcraft cetane boost.