If it is any help, our application is running fine now, thanks to your help. All of our own code runs against our databases fine, and I can run searches from within the webtop using the Solr Pro plugin. Searches on our regular website work fine as well, and of course all of our queries seem to work fine. Sorry I cannot be of any more help!
To answer your question, we are using MySQL 5.7.1, and I have not noticed any of the issues described in this thread.