It is probably a really inefficient query on a page that is hanging it up. The way to debug this is to go to PHPMyAdmin and run the query "SHOW PROCESSLIST".
https://dev.mysql.com/doc/refman/5.5/en/show-processlist.html
That will show you the query or queries that are hung up and then you can know what query you need to optimize. Sometimes you can just add indexes or re-write the queries on the page to make them run more quickly to solve the problem.