Thanks useful information: 
Birds are not necessarily startled by just the preflash, but also High Speed Sync if you are using shutter speeds above X-sync
Tony I think the problem with using 1/1000 as a shutter speed is that it also causes multiple flash pulses. I'm guessing you used High Speed Sync, which unfortunately also sends out multiple pulses to illuminate the frame evenly, so it has the same downside for skittish birds as does a preflash
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