[John Benton] “I’m working with footage that is coming straight off a cheap Aiptek HD camera.”
Unsurprisingly, what you get is a cheap recording format unsupported by a professional editing application.
[John Benton] “. The apple site lists 720P at 60fps as supported.”
Only if it’s in a standard editing codec like DVCPRO HD, XDCAM EX, Apple ProRes, Uncompressed 8 or 10 bit, etc. h.264 is a delivery codec, not an editing codec. It’s a highly compressed codec that’s optimized for low-bandwidth playback, not frame-accurate editing.
Do a quick search of the Cow FCP forum for h.264 and find out how to work with this format (if you must).