I had the same problem regarding syncing the last page read between my iphone app and my kindle touch.
What I did was I reformatted the book using Calibre and changed the personal doc tag to [EBOK].
To change the tag to [EBOK] : Preferences => Conversion => Output Options => Mobi Output => Personal Doc Tag = change [PDOC] to [EBOK].
Then I deleted the problem book from my kindle and from my "manage my kindle" page on amazon, and resent the book to my kindle via email.
I opened it up on the Kindle and went ahead to where I was reading, closed the book and synced. Now when I sync within the book it correctly tells me I am at the furthest page read.
On my iphone I had deleted the app, so I re-installed it and the newly reformatted book appeared in the cloud section. I opened it and it opened on the last read page correctly.
I have since been back to my Kindle and the last page is updating nicely from where I left off in the iphone app.
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