I'm not absolutely sure what is going on here, or what the problems might be, but I'll pitch in and see if I can help.
Equipment: Windows PC running Vista and iTunes 10.6.0.40, using Google Chrome as my default browser.
iPod touch running iOs5.1
iPad 2 running iOs5.0.1
iPhone 4 running iOs5.1
All iDevices are wirelessly connected to iTunes.
I just downloaded a random book from Project Gutenberg (
Project Gutenberg - free ebooks) for the purposes of this test. I also had some DRM free books already on iTunes.
With iTunes book page open, I selected 5 books and dragged them to the iPod. Making sure the whole iPod tab was selected (not just the Books tab), I dropped the books there, then took a look at the iPod. All 5 books were available in iBooks.
Next I opened the folder containing the book I had just downloaded, which was in .epub format, and dragged it into my library, again allowing the whole library to be selected, not just the books tab. iTunes picked up the metadata from the file, and placed it properly in the "Books" section of the library. I dragged the book from the library to the iPad 2, where it is now available for reading.
As I'm not having any problems getting files where I want them, all I can really add to this is that it doesn't seem to matter which version of iOs you are using. iBooks is right up to date, as are Vista and iTunes. Everything appears to be working properly.
Am I missing something?
Just want to add this. Books from Project Gutenberg are copyright free. No book is ever made available on this site unless it is out of copyright, so although you will not get any new stuff here, you can rest assured that anything you download will be legal, decent and honest.