Cummins ISL starting problems

I am working on a kenworth 2007 T800 with a Cummins ISL 350 when I tried to start it it'll crank over good but wont start sometimes it will after about 3 different cranks and sometimes it won't I noticed if I take the fuel separator off that it's only about half full and whenever I fill it up it'll usually start I can hear the primer pump coming on when I first turn the key on there is plenty of fresh fuel and hot batteries but it seems like it's losing Prime I have replaced both fuel filters multiple times it seems like it's worse after it sits for a longer. I did not know if there's a check valve or something my service manager says there's not