CloverETL uses JDBC interface for databases connection. There are 2 kinds of connections:
* connection done by graph
* connection of Server to database (sandboxes, configuration, task scheduling)
By default, for first is used driver from “clover\WEB-INF\plugins\org.jetel.jdbc\lib\mysql”, but it can be changed in connection wizard. For second you probably put own driver on classpath of application server (e.g. [Tomcat]\lib).
So you can check whether versions of driver you use are ok, when used with MySQL 5.5.
In general: minor version change of MySQL (5.1 → 5.5) should be problem-less.