I had similar problems when using Apple iBooksAuthor. I also used an older version of FontExplorer. To fix the problem temporarily, I quit Font Explorer and the cleaning the font cache.
Clean the font cache might be also a solution for you problem.
http://osxdaily.com/2015/01/08/clear-font-caches-databases-mac-os-x/
I had similar problems when using Apple iBooksAuthor. I also used an older version of FontExplorer. To fix the problem temporarily, I quit Font Explorer and the cleaning the font cache.
Clean the font cache might be also a solution for you problem.
http://osxdaily.com/2015/01/08/clear-font-caches-databases-mac-os-x/