I realize this is a old post, but I have a 99 340 and the fuel tanks are not the same size, meaning one tank holds I think between 5 to 10 gals more. I don't remember which side is bigger. Probably the bigger tank is for generator hook up.
I have had this happen with my 99 340 dancer with 7.4s in the summer once in awhile through the years if I haven't run it in awhile, Doesn't do it very often so I really don't worry to much about it. Boat has low 700 hrs on it and still works. One thing to look at, and I'm sure these boats...
Check the electric fuel pump connection on side of engine. This happened on my 340. The connections are known to go bad. I just cut the connection and spliced it together. No problem since.