Why doesn't iBooks save my place between the iPhone and iPad?

Background: I finally bought a fiction book to read on my iOS devices. It's Redshirts by John Scalzi. I bought it from Apple. It was supposed to be DRM-free but wasn't. So the author got Macmillan to send a DRM-free version to anyone who sent a copy of their purchase confirmation. So I deleted the Apple Store version and replaced with the DRM-free epub file.

Problem: My understanding was that when I stop reading on the iPad I could later pick up the iPhone and have the book open up to the place where I stopped on the iPad. But this isn't happening. I've tried placing a bookmark when I finish reading but it doesn't change anything.

Is my original assumption incorrect?

Sync Bookmarks and Sync Collections are both on in iBooks settings on the iPad and iPhone.

I haven't migrated from MobileMe to iCloud yet (still waiting for Bare Bones to get Yojimbo to sync over iCloud). Is that a problem?

Update

I switched over to iCloud and syncing still doesn't happen. My guess is it's because I have two Apple IDs the one I use to make iTunes purchases is not the .mac Apple ID that became my iCloud account.

Solution 1:

iBooks uses your iTunes account to sync bookmarks and places. My wife and I share an account for app and book purchases, so I setup a separate iCloud account for her thinking that her bookmarks would go there. It turns out that I'm wrong, and it's the iTunes store account that stores it. I wish iCloud was the storage location, since the other app settings and backups do work using separate accounts.

Solution 2:

Yeah it is an iCloud / mobile me issue. What you could do is set up a free iCloud account and then perhaps never use it if you do not want multiple accounts, but it would allow you to test it.