John,
I am at my Dad's and have access to his GoFlight throttle quad so I can do some testing. So far this is what I have found out:
After engine 1 is started and you hit E2 to control engine 2, fuel flow is at 0, however, when you move the lever from its E1 position to the cutoff position it takes the value set by the E1 position. One way I think to get around this is after you start Engine 1, press E2 then when you go to move the lever, move it very quickly to the cutoff position and it does not seem to grab the E1 value. You should be able to start engine 2 normally. I can only test this in the PMDG B1900 but it seems to work as long as the fuel lever is not too high up when you start. If you want to monitor fuel flow to E2 use FSUIPCs logging function using offset 2120, putting a check inth e display to FStitle bar so that you can see the value there. If this does not work there is one other thing, does your aircraft have other fuel valves so that you can shut the fuel to engine 2 then open the valve when you are ready to start?
Bud