If your source footage is interlaced ( it looks like DV to me) then make sure you interpret the footage in the project panel - de-interlace ( Fields and Pulldown > Separate fields > Lower field first for DV) and check the Preserve edges.
[Callum Whiteley]"...I can see the clips 'bouncing' slightly every 5 frames or so...."
That's weird. And when video footage acts weird in AE, a common reason is that it's a certain TYPE of video footage:
Dave's Stock Answer #1:
If the footage you imported into AE is any kind of the following -- footage in an HDV acquisition codec, MPEG1, MPEG2, AVCHD, mp4, mts, m2t, H.261 or H.264 -- you need to convert it to a different codec.
These kinds of footage use temporal, or interframe compression. They have keyframes at regular intervals, containing complete frame information. However, the frames in between do NOT have complete information. Interframe codecs toss out duplicated information.
In order to maintain peak rendering efficiency, AE needs complete information for each and every frame. But because these kinds of footage contain only partial information, AE freaks out, resulting in a wide variety of problems.
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