Adobe Media Encoder making blocky videos

The backstory: I have two Mac laptops: an old Powerbook G4/Panther running Imovie 4 and a brand new Macbook Pro/Snow Leopard running Imovie 9.
I've now made several FLVs that play beautifully on the internet: I imported old clips *that had been extracted using the Powerbook/Imovie 4* into my Macbook Pro/Imovie 9, edited the videos in Imovie 9, exported them as standard m4vs, then encoded them into FLVs using Adobe Media Encoder CS4 4.2+. They look terrific.
The problem:
For the first time yesterday, I used my Macbook/Imovie 9 combo to import clips shot with the same exact camera, then did everything exactly the same. The exported m4vs look fine. However, the resulting re-encoded FLVs are badly blocky, as though a mosaic filter was laid on. This is mostly happening when there is any increased motion in the footage.
I tried exporting into .mov then encoding for Flash in the same way, and no difference. The adjustment I'm currently trying is to bypass the presets on AME to enable a 2-pass scan rather than 1. There does not appear to be a keyframe-interval selection option in AME CS4 4.2, or I would adjust that as well. This custom encoding is taking 5 times as long to complete as the preset encoding: over an hour versus 15-16 minutes. It may or may not work, but regardless, I don't have that kind of time - I have a bunch of videos to make.
I'm really sick about this, because my beloved Powerbook has a dying harddrive, which is why I bought the new laptop. I don't want to believe that it was Imovie 4 that was responsible for those lovely videos. Later Macs no longer support Imovie.
Is there something I'm missing that will make AME work with Imovie 9 to eliminate the problem? I know Imovie 9 is a turkey, but it did make those lovely videos with the old clips from version 4. There's gotta be a way.
Thanks in advance.

After playing Youtube go to your temp internet
files and copy the file to HDD which is a mp4.
Add this to the Media Encoder and see if it will work now.
If it still does not work, your ME is prob. not working right.
I sometimes use AME as a converter and it handles mp4 just fine.

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