I figured out what's going on, at least on my Mac, and it has nothing to do with corrupted ini files or anything like that.
If I have the Find/Replace box open when I close an ebook window, the next window I open reverts to default size/position. Re-sizing/re-positioning the window then closing it, does not help. The new size/position will not stick as long as the Find/Replace box is open when I close.
However, if I close the Find/Replace box before I close the ebook window, then the size/position is saved, and the next ebook window opens in the same size/position as the last window opened.
Steps to reproduce (on my Mac):
I don't know if this is known and expected behavior or something peculiar to my Mac. I also suspect this was happening in 0.9.10 and is why the window would sometimes "mysteriously" (to me) revert to default window size/position. I usually keep the Find/Replace box closed for a cleaner window, so on the less-common occasions that I leave it open when closing, it would result in the next ebook "inexplicably" opening in the default window position.
In any case, closing the Find/Replace window before closing a window solves the problem. I report this in case it's helpful to anyone