Time-lapse flicker unchanged after Color Stabilizer

I shot a sequence of still photos of a cluster of roses blooming in front of a blue screen for creating a time-lapse clip, my first time to try that.  I have an NTSC-sized comp that fills the frame nicely with just one of the roses.  As expected, there is flicker due to imprecision in the camera's aperture, and the rumor is that AE's Color Stabilizer effect should fix that.  I have Keylight to key out the blue, and also TimeWarp to speed it up because the rose took longer than I thought to open (although that's optional, as I can just make the clip at its original length and speed it up in PPro when I combine it with backgrounds), but I made sure to put the Color Stabilizer below those other effects in the timeline - that should mean it is applied first, right?  The Color Stabilizer in is "Brightness" mode, and because the rose's petals move, I put the "Black Point" on the blue screen.  But it still flickers - it doesn't look like there is any improvement over not using the effect at all.  Am I doing something wrong?  Naturally, if the Color Stabilizer was being applied after Keylight, it wouldn't work because the background would already be erased, but I think it should be applying it first.  If I have to put the Black Point on some part of the rose, I will have to chase it with a bunch of keyframes, and it may still not work right.  Recommendations?
I wish there was an effect that would simply look at the whole frame's brightness and smooth each frame to a running average of several frames in a row, but as far as I know, such an effect doesn't exist.
Additional info: AE CS4 on Windows XP. The photos were for 1 second each @ f-8 with a Canon Powershot S3-IS, if that matters.

If the lighting and background are constant, there's nothing for Color
Stabilizer to do, you should not have needed it at all.
That would be true if I was shooting with my video camera (which I have done for many a sunrise or other less-than-one-hour time-lapses.  But the problem is that most still cameras do not keep their aperture set while waiting between shots, and even in manual shooting mode with a specific f-stop, there will be slight variations.  The flicker isn't caused by my subject matter, but by my camera.
In my case, I'm actually pretty pleased that my camera did as well as it did, considering that it's not an SLR.  The flicker is not nearly as bad as some examples I have seen on the web.  For your benefit, I made two half-resolution Quicktime file of the same 4 seconds of the middle of the sequence - this one has no effects at all, and this one has not just one but two effects added that are rumored to be helpful in reducing flicker: Color Stabilizer in "brightness" mode with the "black point" on the background, and Auto Levels with a Temporal Smoothing setting of 1 second.  (Even at half-resolution and only four seconds, the files are still over 14MB each, because they contain the full frame rate of 29.97 fps, so be patient with the download.)  To my naked eye, I can't see much difference.
I'd have
processed the individual stills in a batch in Photoshop first, leveling
all variables.
How does one do that?  I do have Photoshop (CS2),  but I'm not much of a Photoshop expert and have no idea how to get it  to compare levels between even two files, much less do such comparison  in an batch fashion between thousands of files.
Thanks for the link.  I didn't see anything directly relevent at first glance (deflicker discussions center around using VirtualDub on a progressive video file, but my source is 3000 still photos, my destination is interlaced DV-encoded video, and I don't really want to process and resave it multiple times if I can avoid it).  But when I have more time, I'm sure I could learn lots about time-lapse in general by reading the forum threads.

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