Did those that download, download sequentially and then stop downloading or is it hit and miss?
You might try changing the meta data on a couple of books that will not currently download and see if they suddenly download before you attempt any global fix. Can you trace back to which books where lit vs html and/or the source that could give you a clue on why.
I have a library of over 900 ebooks in Calibre and have never run into this. Mine all seem to download easily although I don't read that many on my iTouch.