The best I could do is to turn off INFO level logging for the class that generates the log entry (via the Glassfish console).
The problem is the RichFaces upload filter uses the servlet getRequestParameter method ahead of the normal JSF lifecycle process where the character encoding is set, and as the logged message suggests calling getRequestParameter implicitly sets the encoding, resulting in the message when JSF attempts to set encoding explicitly.
Some questions related to turning off logging (from the Jira entry it seems like there's currently no solution?) - what is the "class that generates the log entry" and how do I disable logging for that class, i.e. menu steps...?
The class that does the logging is : org.apache.coyote.tomcat5.CoyoteRequest
From the admin console select "Application Server", "Logging", "Log Levels".
Turn the "Web Container" to level SEVERE (it is logged as a WARNING, not INFO as I first said).
To apply this less broadly, add a new property with name the class name above, and value SEVERE.
Thanks, this solves the problem.