Yes, David, and you’re definitely on to something. I came back to the project today with a clearer head. On closer inspection, it seems that none of the clips are actually missing. They just dump out early (usually after only one frame, which makes them appear all but invisible when zoomed out – but some run for a second or two before ending early). Furthermore, the master clips in the bin created by Media Manager all have the appropriate runtimes. As a result, I’ve been able to just extend the shortened clips on the timeline to their appropriate lengths (adjacent clips all start at the right in-point, both for the clip and the timeline).
But, to your question, all of the affected clips were either slowed down or sped up, using FCP’s Speed command (Apple-J). However, there were other speed-altered clips in the timeline that were not affected. Also, there are several stills in the project, which were unaffected.
So this is a known problem, maybe?
Thanks again for your assistance.