There are a few things to check:
Make sure your tanks or fuel caps are vented
Are you drawing from both tanks at once, or are they valved seperate.
The pickup tube in the tanks could be partially clogged, broken, or sucking air
The fuel pump could be dying on you.
Restriction in filter/water seperator.
Fuel Line size too small.
Just some things to check.
T.J.
www.tjsperformance.com