I had major issues with 1.9.16 - one of which was the problem you describe.
I have found 1.9.17 much better than 1.9.16 although quite a few people report problems with no top margin on their side loaded epubs. As I use very small margins this doesn't bother me. Your view may be different.
I have also found that my Touch works best with about 100 books or less on it. I don't use an SD card as many people have reported problems there.
I wish I could have all my books on the Touch as when I travel for several weeks at a time I would like to be able to choose from my full library - not just the 100 or so books I thought I might feel like reading a few weeks ago.
However when I am away from my computer I don't want to do anything that could trigger a reset so I play it very safe.
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