I've put together a Mac OS X 10.11 VM instance (on VirtualBox on my Windows8), with the latest released calibre (2.55.0) and FanFicFare (2.3.1), plus EpubMerge and EpubSplit.
I did not see the problem reported. I updated to Mac OS X10.11.4 (the latest version) and still did not see the problem. That pretty much exhausts my resources for trying to figure this problem out.
I like @davidfor's suggestion. If there are other weird Mac problems going on, it's a good chance they are related. Please try the beta calibre version and report back whether it works.
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