I shot two sample clips at 25p (one with pre-record on and one without it) and imported them into FCE4 (using AIC 1920x1080i50 Easy Setup) and iMovie '08. While both clips played correctly in the log & transfer preview window in FCE4 and the iMovie 08 import preview window, I get the reported flashes of green and breakup intermittently through the first 5 seconds of each clip in both programmes. There was no obvious difference between the clip with pre-record and the one without.
I suppose one work-around would be to make sure to fire off 5 seconds at the beginning of every take when shooting 25p. A pain to be sure, but at least that way you'll know you're recording usable video after 5 seconds.
Given that there is no AVCHD–AIC 1920x1080p25 Easy Setup in FCE, my guess is that progressive AVCHD isn't supported - though I expect that the SD9s 25p is really 50i in disguise. I wonder how people with HF100s have got on with this . . .
Andrew.