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Another Mac user here...Pixelmator is another option that is relatively inexpensive and near-Photoshop functionality.
I can't explain the funny overlapping. What I usually try to do is make sure that when I take multiple sets of subs that the camera orientation is more or less the same. A couple of degrees doesn't matter all that much, as DSS will happily stack em all but the more they don't match the more it crops out in intersection mode.
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