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Have you run software update? I've heard of this problem somewhere else some time ago and thought support for the 24p / 25p mode on the SD9 had been sorted.

Andrew.
 
Hm. I'll have to try this out with my SD9 to see what gives. In the meantime, make sure you don't have the 3-second pre-record mode selected on your SD9. Apparently that screws things up right royally. Also, check that you don't have a codec by the name of Perian installed.

If I have a chance to test this today I'll get back to you.

Incidentally, it's definitely 25p you're shooting? Just wanted to check, since mine is a 50i/25p model, too.

Andrew.

Also: have you seen this? http://discussions.apple.com/thread.jspa?messageID=8291921. May or may not be relevant to your situation.
 
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.
 
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