I've read several articles about this error occuring for slow queries and things to do with connection pooling.
My problem has nothing to do with those. It's a simple connect to database, run query, process resultset. Nothing fancy with threads or anything, very simple table as well. The webapp is very basic.
The article you linked to suggests Tomcat does connect to mySQL but loses it later on when the queries get slow. For me tomcat doesn't connect to mySQL at all, just throws the error I mentioned. But a standalone java app can use the database with no problems. My guess is tomcat is being silly somewhere, I just don't know where.