You may have a little bit of water in the filter that has accumulated over time. Just drain it and try again. It shouldn't be a problem after you've drained it unless there really is a lot of water in the system (from condensation in the tank, from the commercial fuel, or the biodiesel). Check out page 281 of the 2005 owners manual:
Quote:
Diesel fuel is seldom completely free of water. To prevent fuel system trouble, drain the accumulated water from the fuel/water separator using the fuel/water separator drain provided.
Instructions can be found here:
http://www.jeepkj.com/forum/f196/routine-draining-water-fuel-water-separator-crd-eng-26609/Or on page 14-49 of the '05 Service Manual.