You're probably running it way rich. The factory pumps, at least the BN2 pumps, pulse. They squirt a touch of fuel, pause, squirt, pause, squirt, pause, etc. On the later model pumps (the only one I have direct experience with) you can tune the amount of fuel that is released with each pulse. The manual I linked you to has testing procedures for setting the correct amount of fuel per hour. Based on the recommended settings, with me burning less per hour I'm running "lean".
What kind of pump are you using? If I can find a useable pump (that's less then $200) I have about 6 gas heaters ready to go for sale.
-Dave