Andy,
This article may be useful to you.
In short, Calibre creates epubs that work; however, they are not necessarily fully compliant with epub spec. Also note this note from that article,
"Tip #4: Even though the files properly validate with an EpubCheck site and validate with iTunes Producer, they’re not being tested for everything that Apple’s system might require. Validation doesn’t necessarily mean valid."
So, even if you check your epub with EpubCheck, it is no guarantee that it will pass Apple's muster.
On a different note, why doesn't Calibre properly handle <blockquote> in epubs?