I believe I ran into the same problem as rfog yesterday and I do think it may be related to vertical scrolling. I don't normally use this feature but I do occasionally use it in conjuction with text-to-speech.
Marvin _was_ updating the sync file according to the timestamp but the value was stuck at 15% most of the day even though I was more than halfway through the book and back in paginated mode. I believe closing Marvin completly fixed the problem for me.
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