I'm exporting a package to send to my publisher. Package doesn't include all links. I've tried several times with same result. The few that do export are .psd, .ai, .pdf and jpeg so it's not a particular file type it's having trouble with. Other chapters I packaged worked OK, it's just two chapters that are having trouble.
Sounds like it's probably an issue of "illegal" charater in the filename or a folder name.
Make sure ID is fully patched, as well.