If you are not running a elect fuel pump between the fuel tank and the pump on the motor that may happen. I had another boat that had saddle tanks and the same thing would happen. I finally installed a electric pump and that seemed to fix the problem.
I ran the lines to a "Tee" connection in between the fuel tanks and the new electric pump and then let the elect push the fuel to the motor's fuel pump.
There are pro's on here that may know something else that may help you.
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Tis better to be quiet and thought a fool than open your mouth and prove it!!
1991 V-20 cuddy I/O 350 volvo duo prop, 1998 15ft Grumman 9.9 Johnson 
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