Generally speaking it is a bad idea to have your flash turned on. Most cameras will NOT let you take a second picture until the flash recharges, which limits how fast you can trigger the shutter. When your battery is low, this can extend out to 5 or 10 seconds between shots.

StarskiPZ gives the other reason to leave the flash off... light reflecting off the plane can bounce back into the lense causing lense flare, loss of contrast, etc.

A better way to be sure you got a picture is to be confident that your triggering method is reliable, and then just trust it!

C.F.