Thanks Kovid - your reputation for quick response is deserved.
I suspected you'd need a sample to look at, but I thought the symptom might be common.
The pdf in question is very large (~80MB) so I am uploading it to my webserver and will post the link as soon as it is available. Thanks for taking the time.
I was concerned that epub would not be suitable for books with many illustrations, but I have been encouraged by some I have seen recently. I'll be working on this one to learn best practices.
Link in next post.