I have a 2011 chevy silverado 3500hd, crew cab, 8' bed. Today with 11,500 miles I had 2/3 tanks of diesel and I topped it off at a Flying J gas station. Within 50 miles I got the "Water in Gas" warni...
I got my money on the sensor system having a problem. However instead of messing around on the keyboard I would catch some fuel and look. Water will be totally separated and show up in the bottom of the catch jar.
By the way, when I had a diesel I put an extension hose on the bottom of the drain tube and zip tied it secure so I always had easy access.
Flying J just could not afford to be pumping water in those big company rigs. :h