I once had the same problem with my Cummins 8.3 ISC. The last shop where I had it serviced changed both filters but, they used too small a micron filter for the second filter -- I think it was a 4 micron filter. Cummins recommends that BOTH filters be 10 microns -- I changed out the fuel filters to both being 10 micron filters and no problems since.
Dave and Karen -- '02 Ultimate Advantage 36 C, 350 HP Cummins, Allison 3060 Tranny
'07 Ford Escort, Brake Master 4160, '13 Ford Edge, InvisiBrake