No, this isn't due to an issue with the epub itself. This is due to a firmware change in the latest firmware, which seems to now generate covers from the first page rather than getting it from the package document. I haven't
tested this much, and it may not apply in all cases. I'm planning to
write a cover extractor later to work around this issue (probably next time I import a bunch of books).
Update: I just read back through this thread, and what Jon mentioned about enabling cover uploading in Calibre would have the same result, assuming you use Calibre for your ebooks.