My issue isn't a side loaded issue, but...
I'm running 3.1.1 on an iPad 3 and have a Personal Document that was emailed to my Kindle address, thus placed in the cloud, then downloaded to my KT. All bookmarks and highlighting done via the KT along with furthest page read are transferred to the iPad. However none of the bookmarks and highlighting done via the iPad nor the furthest page read are transferred to the KT. The sync icon on the iPad is grayed out for this book. The same issue occurs with the book on my iPod touch, except the sync icon on the iPod touch is not grayed out for this book, however pressing seems to have no effect.