Not sure on that one. Recently I had a bubbling noise, but it was behind the glove box. Turned out to be air trapped in the heater core. Have someone shut your truck off with the hood up while you stand outside with a mechanic's stethascope or use a piece of heater hose to determine exactly where it's comin' from.
Use the stethascope or heater hose and let us know what you find out. Almost sounds like you're losing your fuel system "Prime". If you "key on" "Key off" several times before you crank it over, does it start right up?