Karin, are you using one of these auto flush valves, or just a regular manual flush valve? Is your booster on when you flush the membrane? My understanding is that the auto flush valve when used with a booster pump and tighter restrictor can help to mitigate membrane fouling while increasing efficiency by "power flushing" the membrane automatically at full boosted water pressure both on startup and every hour of operation (flushing is for 15 seconds).

http://aquatec.com/auto-flow-restricters.html