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Coming back last weekend from picking camper up I got fuel at station, seemed reasonably busy, drove about 45 minutes, stopped and ate dinner. As soon as I started truck, WIF message appears. I drain separator, still shows message, I drive to nearest place that has fuel filter (autozone). Change both lower and upper filters, start it and no light, drive about another 45 mins home no light. Shut truck off come back out next day to park Camper and WIF light is on again, I drain separator again with no change, drain upper filter no change. So I changed both filters again, this time immediately after start up light comes on again. There is no way the separator got that much fuel in it again, truck all this time never once ran rough and was never low on power other than when it was in limp mode when light first came on. I was pulling a 15,000lb campers at time.
Was there any water in the fuel that you drained? It sounds like the system isn't working right. I think there was another forum member that had a similar issue and it was a sensor that went bad.
If in fact you haven't actually found any water in your fuel sample, pull the connector from the WIF sensor and apply some dielectric grease and plug it back in. Sometimes the connection can be problematic.