If the truck sat for a while, it could be a deposit from old fuel. I had a bad sticking rack issue on a Detroit from old fuel, it ran fine until I took it up to operating temp then the rack stuck the next time I ran it. The excess fuel from that machine did make my 7.3 with a DB2 pump run a bit funny for a while but mixing a quart of Dexron with each tank for a few tanks cleared that up.
The ATF might work in your truck as well, if not try some Diesel Kleen or even run a couple cans of purge through it.