Ok, I did a little playing around and discovered a few things.
First, I found out that if I deleted an ebook from the iPad it remained in iTunes (expected) and did not re-sync automatically next sync (preferred), but it was a pain to get it to sync again when I wanted it too.
When I checked my Books sync preferences it staid it was syncing all books. So I turned it off. It asked if I wanted to remove books, and I said yes. But I did not sync, I just turned it back on. At that point it came up as syncing selected books. When I forced it back to all books and synced again my stubborn book was synced back to the iPad again.
Based on this I'm guessing that your iTunes is actually syncing selected books, even though it may be stuck on saying it is syncing all books. So give this a try.
Change your Books sync to selected books. Your already synced books should already have checkmarks next to them. Select one of the books that is not syncing, and try a sync. If that book gets synced the way it should, go back to the Books sync page and select all books again. Try syncing again and see if it now works.
For your second problem, I actually ran into this first, and I did it the same way you did. I mailed myself a couple of ebooks, one pdf and an epub I had converted using Stanza some time ago. The epub didn't sync back to iTunes.
I haven't figured out how to fix this yet, but I did notice something odd. When I expand the iPad in iTunes and look at the Books list the ePub does not show up. This despite that fact that I can open and read it on the iPad.