Turns out this was caused by multiple SWFObjects on the same page. The code that wrote them out wasn’t built for multiple objects, so it always created a container div with the same ID, then wrote the object into that div. So the movie wasn’t getting shrunk – it was getting overwritten by a smaller similar-looking one.
Fixed by changing the code to increment a counter of Flash objects so that separate IDs are used each time.
Part of the point of a buglog, I guess, is that you get to keep track of the embarassing ones too =]