It works ok here with Win 8.1 (64 bit) which is probably not useful news in itself.
However, the following may provide a clue to others with more detailed knowledge of Sigil's innards.
I did a couple of tests with large books (7 to 10+ MB) and in every instance it ran quickly until indicated the same 87% completion as you mention, when it paused. But in my case, after pausing, it then ran to completion. So in your case it seems to be failing at what appears to be a point of intensified processing activity.