Hi, I'm sorry for late response. I downloaded Mavericks yesterday and had the same problem.
But now I found the solution.
I only turned on "sync bookmarks" on my iPhone.
On my Mac, I did the same in "Preferences". I also connected to my account under the "store" tab.
After that, if i bookmarked a page on my iPhone, I went back to my library of books. "where all the books are".
On your Mac computer, you should go to the main page "the entire books on your library are". And after open the book you're reading.
If you're bookmarking a page on your computer. Go back to the main page after your bookmark. On the main page of your iPhone iBooks, go to the book you're reading and open it. Your bookmark my should be there.
Remember, you have to connect to your account (on your mac) to do all this.
I hope it helped
OK so I tried it today with a book purchased on iTunes... and a sideload book. Both worked.
On your iPhone, you need to enable "sync bookmarks".To do this on your Iphone. (sorry if words are not the same, i use another language on my Iphone and Mac.)
Open your preferences tab. Scoll down and you should see the iBooks images. Open it. Then you should see to sync my bookmarks square. Enable it (by pressing once.)
Now on your Mac, by default the computer enables sthe syncing of bookmarks. If It isn't just go to the "preference" (under the iBooks word on the top of your screen). Where you see the word synchronize with my bookmarks. You enable it. Now you have to close the window.
Youhave to connect to your Apple account (with your apple ID) like you do on your Iphone to get apps. To that just go to the "store" tab (on the top) and choose the "connect" (something like that). After you connected open your book (anyone you want). Start reading. Make your bookmark (which is tapping on the ribbon on your top right of the window) The Ribbon becomes red when bookmarked like your Ibooks in Iphone.
Open your Iphone and you should have a bookmark.
The only problem I saw when doing a bookmark with a sideloaded book is that when i bookmarked on Mac.....the bookmark on my Iphone was a few pages either further or before. Must be because of the font styles on my iPhone.
Hope this helps